We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Central is beta-diversity-the component of regional diversity that accumulates from compositional differences between local species assemblages. Two examples are demonstrated, using the data (one for abundance data and the other for incidence data) included in the package, to illustrate all R functions and graphical displays.read more read lessĪbstract: To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. (iv) Comparison of estimated point diversities for a specified sample size or a specified level of sample coverage. (iii) Assessment of sample completeness (sample coverage) across multiple samples. (ii) Asymptotic analysis: comparison of estimated asymptotic or true diversities. Several applications of the iNEXT packages are reviewed: (i) Non-asymptotic analysis: comparison of diversity estimates for equally large or equally complete samples. Two types of biodiversity data are allowed: individual-based abundance data and sampling-unit-based incidence data. We present an R package iNEXT (iNterpolation/EXTrapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity). We briefly review the conceptual background of Hill numbers along with two approaches to standardization. The sample-size- and coverage-based integrations of rarefaction (interpolation) and extrapolation (prediction) of Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages. Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. 3: (a) (upper panel) Sample-size-based rarefaction (solid lines) and extrapolation (dotted Table 2: The theoretical formulas and analytic estimators for rarefaction and extrapolation of Hill numbers based on incidence data for q = 0 (first row of equations), q =1 (second row), q = 2 (third row) and any integer order q> 2 (fourth row), given a reference sample1 with the observed Hill numbers obs.5: (a) (Upper panel) Coverage-based rarefaction (solid line) and extrapolation (dashed line) 4: Plot of sample coverage for rarefied samples (solid line) and extrapolated samples (dashed Each curve was extrapolated up to a doubling of its reference sample size 7: Plot of sample coverage for rarefied samples (solid line) and extrapolated samples (dashed line) with 95% confidence intervals for tropical ants sampled from five sites (data from Longino and Colwell 2011). 6: (a) (Upper and middle panels) Sample-size-based rarefaction (solid lines) and 8: (a) (Upper and middle panels) Coverage-based Rarefaction (solid line) and extrapolation (dashed line) plots with 95% confidence intervals for tropical ant diversity based on Hill For the Girdled treatment, Sobs = 26 species, n = 168 individuals for the Logged treatment, Sobs = 37 species, n = 252 individuals. Spider species abundance frequency counts in two canopy manipulation treatments (Ellison et al.
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