Abundance‐Based Similarity Indices and Their Estimation When There Are Unseen Species in Samples

By A. Chao, R. Chazdon, Robert K. Colwell, Tsung‐Jen Shen. Biometrics, 2006

631 citations recorded by the source corpus.

Subfields: Ecological Modeling, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/c0942efa5ed5112219226d505b58d388010f981d

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In Ecological Modeling

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Citations in the corpus

Secondary forests of central Panama increase in similarity to old-growth forest over time in shade tolerance but not species composition (2013, background): “For further details about similarity indices, refer to Chao et al. (2005, 2006) and Jost (2006).”
The Gut Microbiome Modulates Colon Tumorigenesis (2013, background): “The abundance-based Jaccard dissimilarity index indicates the fraction of all sequences that affiliate with OTUs that are shared between two communities and was used to calculate the fraction of OTUs that were shared between donor samples and germfree recipient samples (48).”
A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity (2010, background): “…usually researchers are interested in habitats and regions so extensive that full species inventories are a practical impossiblity, so that obtaining accurate estimates of alpha and gamma diversity is a major concern (Colwell and Coddington 1994, Plotkin and Muller-Landau 2002, Chao et al. 2006).”
MEASURING BEE DIVERSITY IN DIFFERENT EUROPEAN HABITATS AND BIOGEOGRAPHICAL REGIONS (2008, methodology): “We used the novel Chao-Sørensen abundance-based estimator as a measure of similarity, because in comparative studies this estimator proved to be less biased than classic indices of similarity (Chao et al. 2005, 2006).”
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics (2015, methodology): “The abundance-type index contemplates abundance similarity, thereby treating individuals not species equally; some examples are the Morisita-type and Bray–Curtis dissimilarity indices (Chao et al., 2006).”
Interpretable Random Forests via Rule Extraction (2020, methodology): “Such a metric is known as the Dice-Sorensen index, and is often used to assess variable selection procedures (Chao et al., 2006; Zucknick et al., 2008; Boulesteix & Slawski, 2009; He & Yu, 2010; Alelyani et al., 2011).”
SIRUS: making random forests interpretable (2019, methodology): “We take advantage of a dissimilarity measure between two sets, the so-called Dice-Sorensen index, often used to assess the stability of variable selection methods (Chao et al., 2006; Zucknick et al., 2008; Boulesteix and Slawski, 2009; He and Yu, 2010; Alelyani et al., 2011).”
Associations between species and groups of sites: indices and statistical inference. (2009, methodology): “The second generalization is intended to be used with individual count data, and it is equivalent to the one proposed by Chao et al. (2006) for site similarity measures.”
Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures (2006, methodology): “Chao1 richness estimator is a function of the number of OTUs observed once or twice in a sample (3), the estimator of the fraction of sequences in shared OTUs is a function of the number of shared OTUs that are observed at least once or twice in the community being analyzed (5, 4 ):”
Thirty years of progeny from Chao’s inequality: Estimating and comparing richness with incidence data and incomplete sampling (2017, background): “…assemblage overlap and forms a basis for constructing various types of beta diversity and (dis)similarity measures, such as the classic Sørensen and Jaccard indices (Colwell and Coddington, 1994; Magurran, 2004; Chao et al., 2005, 2006; Jost, Chao and Chazdon, 2011; Gotelli and Chao, 2013).”
FunGene: the functional gene pipeline and repository (2013, methodology): “Probe Match (Myers, 1999; Cole et al., 2005) performs a search against the selected nucleotide sequences (subjects) for matches to the entered oligonucleotide sequence (query).”
Deciphering Diversity Indices for a Better Understanding of Microbial Communities. (2017, methodology): “, relative richness; measurement of OTUs actually observed in samples), whereas ACE (Abundance-based Coverage Estimator) and Chao1 indices are used to estimate richness (estimated richness; measurement of OTUs expected in samples given all the bacterial species that were identified in the samples) [”