betapart: an R package for the study of beta diversity

By A. Baselga, C. Orme. 2012

2,080 citations recorded by the source corpus.

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

View Paper: https://www.semanticscholar.org/paper/f31ca383c856b7175cb4a89fc55b4f617af154bd

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In Ecology

In Ecology, Evolution, Behavior and Systematics

In Nature and Landscape Conservation

Citations in the corpus

The impact of even‐aged and uneven‐aged forest management on regional biodiversity of multiple taxa in European beech forests (2018, methodology): “…80 100 120 SP −19%, TG −17%(i) 20 60 100 180140 Spiders Beetles True bugs Bats Birds Vascular plants beta.sample in the package “betapart” version 1.3 (Baselga & Orme, 2012), for Mantel test the function mantel in the package “ecodist” and for multiplicative partitioning and estimating…”
Hydrological stability drives both local and regional diversity patterns in rock pool metacommunities (2015, methodology): “…in metacommunity composition captured in the S ø rensen dissimilarity index (betaSOR) was partitioned into components that correspond to turnover (betaSIM) and nestedness (betaSNE), respectively, according to the method developed by Baselga (2010) and implemented by Baselga and Orme (2012).”
Comparing methods to separate components of beta diversity (2015, methodology): “We however reserve the term ‘family’ for the set of measures derived from either Jaccard or Sørensen indices (i.e. Sørensen and Jaccard families as originally termed by Baselga 2012; Baselga & Orme 2012).”
Disentangling the correlates of species and site contributions to beta diversity in dung beetle assemblages (2018, positive): “This function computes the overall dissimilarity (here measured as Jaccard dissimilarity) between the 2 years, and partitions it into its turnover and nestedness- resultant components (Baselga, 2010, 2012).”
South‐western Atlantic reef fishes: Zoogeographical patterns and ecological drivers reveal a secondary biodiversity centre in the Atlantic Ocean (2018, methodology): “Multiple- site dissimilarity measures of the nestedness and turnover components of the Jaccard dissimilarity index were carried out between neighbouring sites within the SWA using the method described by Baselga and Orme (2012).”
BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity (2015, methodology): “The package betapart (Baselga & Orme 2012) implements alternative methods, although we disagree with the methodological framework developed by these authors (see Carvalho, Cardoso &Gomes 2012; Carvalho et al. 2013; Cardoso et al. 2014c).”
Beta diversity of diatom species and ecological guilds: Response to environmental and spatial mechanisms along the stream watercourse (2018, methodology): “All analyses were performed with the packages vegan (Oksanen et al., 2016), betapart (Baselga & Orme, 2012) and effsize (Torchiano, 2016) of R Statistical software (R Development Core Team, 2016).”
What drives study‐dependent differences in distance–decay relationships of microbial communities? (2021, background): “We echo the call of Green and Bohannan (2006) for microbial ecologists to exercise more care in their choice of dissimilarity metrics, especially given that many of these new metrics are implemented in popular and freely accessible software, such as R (e.g., Baselga & Orme, 2012).”
Does pollen-assemblage richness reflect floristic richness? A review of recent developments and future challenges (2016, positive): “They 1051 further investigated beta diversity by decomposing it into two components – nestedness and 1052 turnover (Baselga, 2010; Baselga and Orme, 2012; Legendre, 2014).”
Separating the two components of abundance‐based dissimilarity: balanced changes in abundance vs. abundance gradients (2013, methodology): “Mat. and to be implemented in package betapart; Baselga & Orme 2012) to compute the dissimilarities, the vegan package (Oksanen et al. 2011) to assess the significance of relationships using Mantel tests, and the boot package (Canty & Ripley 2008) to estimate frequency distributions of slopes,…”
Partitioning abundance‐based multiple‐site dissimilarity into components: balanced variation in abundance and abundance gradients (2017, positive): “The new indices can be computed, using the R package betapart (Baselga & Orme 2012).”
Geographic patterns and environmental correlates of taxonomic and phylogenetic beta diversity for large‐scale angiosperm assemblages in China (2020, methodology): “We used the following R packages for computing β-diversity metrics and conducting permutation-based statistic analyses: betapart (Baselga and Orme 2012), vegan (Dixon 2003), ecodist (Goslee and Urban 2007), picante (Kembel et al.”
Functional homogenization exceeds taxonomic homogenization among European fish assemblages (2014, methodology): “Statistical analyses were carried out using R (R Core Team, 2013), including the libraries betapart for computing dissimilarity indices (Baselga & Orme, 2012; Baselga et al., 2013) and ecodist for MRM analyses (Goslee & Urban, 2007).”
Habitat filtering determines the functional niche occupancy of plant communities worldwide (2018, positive): “However, the convex hull method is relatively more sensitive to outliers than the hypervolume method (see an example in Appendix S2) and is unable to calculate the union of multiple (more than 10) convex hulls (Baselga & Orme, 2012), and thus was not applicable for our study.”