Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size.

By A. Chao, L. Jost. Ecology, 2012

2,016 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/8cea92ac73ffa0cf8cd0b6eb2c8f5aa70371ba98

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology, Evolution, Behavior and Systematics

In Genetics

In Nature and Landscape Conservation

Citations in the corpus

Fuzzing: A Survey for Roadmap (2022, background): “This motivates Böhme et al. [17, 20, 21] to formulate fuzzing processes as a species discovery problem [32, 33, 52].”
EstimateS turns 20: statistical estimation of species richness and shared species from samples, with non‐parametric extrapolation (2014, methodology): “(2012) to the full set of Hill numbers and to coverage-based rarefaction (Chao and Jost 2012).”
Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers (2014, methodology): “Alternatively, to make fair comparisons among samples, ecologists have used rarefaction and extrapolation to compare species richness at a standardized sampling effort or sample completeness (as measured by sample coverage) (for a review, see Chao & Jost 2012, Colwell et al. 2012).”
Precipitation mediates the effect of human disturbance on the Brazilian Caatinga vegetation (2017, methodology): “We used the coverage estimator recommended by Chao & Jost (2012) to estimate the accuracy of diversity inventories: Ĉn ¼ 1 f1n ðn 1Þf1 ðn 1Þf1 þ 2f2 where f1 and f2 are the number of species with one individual and with two individuals in the sample, respectively, and n is the number of…”
Sampling networks of ecological interactions (2015, background): “Symbols as in Table 1; N, number of records; Chao1 and ACE are asymptotic estimators for the number of distinct pairwise interactions I (Hortal et al. 2006), and their standard errors; C, sample coverage for rare interactions (Chao & Jost 2012).”
Measuring temporal change in alpha diversity: A framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT.3D standardization (2021, background): “Chao and Jost (2012) derived an interpolated coverage estimator ̂C(m) for any rarefied sample of size m n, and an extrapolated coverage estimator ̂C(n + m ∗ ) for any augmented sample of size n + m*.”
Chronic anthropogenic disturbance drives the biological impoverishment of the Brazilian Caatinga vegetation (2015, methodology): “…among plots and ontogenetic classes (ranging from 20% to 99%), our estimates of species richness could be biased by differences in sample completeness (Chao & Jost 2012), particularly because species richness is sensitive to variations in the number of singletons and doubletons (Jost 2006).”
Thirty years of progeny from Chao’s inequality: Estimating and comparing richness with incidence data and incomplete sampling (2017, background): “Chao and Jost (2012) indicated that a sample of a given size may be sufficient to fully characterize a low-diversity assemblage, but insufficient to characterize a richassemblage.”
Temporal scale‐dependence of plant–pollinator networks (2020, background): “As an additional aspect of sampling completeness, we also estimated sampling coverage (Chao and Jost 2012) at the level of plants, pollinators and links for each network.”
Quantifying sample completeness and comparing diversities among assemblages (2020, methodology): “Chao and Jost (2012) and Chao et al. (2014) adopted this sample coverage as a standardization criterion to compare diversity among assemblages for incidence data.”
Estimating diversity and entropy profiles via discovery rates of new species (2015, methodology): “By applying slope estimators derived from an improved Good–Turing frequency formula (Chao & Jost 2012), we obtain a more accurate continuous diversity and entropy profile.”
Biodiversity change is uncoupled from species richness trends: Consequences for conservation and monitoring (2018, background): “…richness among sites or time periods comparable when the size of the regional species pool differs, as the same observed absolute change creates a higher relative difference in a community consisting of a few species than in a diverse community (e.g. Chao and Jost, 2012; Chase & Knight, 2013).”