BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

Abstract

1. Novel algorithms have been recently developed to estimate alpha and partition beta diversity in all their dimensions (taxon, phylogenetic and functional diversity -TD, PD and FD), whether communities are completely sampled or not. 2.The R package BAT -Biodiversity Assessment Tools -performs a number of analyses based on either species identities (TD) or trees depicting species relationships (PD and FD). Functions include building randomized accumulation curves for alpha and beta diversity, alpha diversity estimation from incomplete samples and the partitioning of beta diversity in its replacement and richness difference components. All functions allow the rarefaction of communities. Estimation methods include curve-fitting andnon-parametric algorithms. Beta diversity indices include the Jaccard and Sørensen families of measures and deal with both incidence and abundance data. Two auxiliary functions that allow judging the efficiency of the algorithms are also included. 4.Several examples are shown using the data included in the package, which demonstrate the usefulness of the different methods. The BAT package constitutes an open platform for further development of new biodiversity assessment tools.

Global Island Monitoring Scheme (GIMS): a proposal for the long-term coordinated survey and monitoring of native island forest biota

“…The protocols listed in Table 1 for vascular plants, birds and mammals are comparatively less time consuming than those for bryophytes and arthropods (BRYOLAT and COBRA protocols), which were originally designed for the inventory of biodiversity, and thus need to be optimized for monitoring. To optimize the protocols for the purpose of monitoring, we took several steps building on previous work by Cardoso et al (2016), and developed a version of BRYOLAT-Monitoring and COBRA-Monitoring protocols (see Appendix S2-Protocols) using the R package BAT (Cardoso et al 2015).…”

Earthworm diversity and ecosystem services in agriculture: Choosing appropriate taxon indicators and measurements

“…For the statistical analysis in R 3.1.3 (R Development Core Team 2015) the packages "BiodiversityR 2.5-1" (Kindt and Coe, 2005) and "iNEXT 2.0.1" (Hsieh et al, 2014) were used. (Cardoso, 2015) Figure 2 Relation between subsamples and species richness for sampling units and a range of sampling effort (gray: interpolated; black: observed; white: extrapolated). The dashed line indicates an estimated species richness .…”

Wild Herbivore Grazing Enhances Insect Diversity over Livestock Grazing in an African Grassland System

“…domestically grazed PA, which does not exist by definition). Alpha diversity (rarefied observed species richness) was calculated using the BAT package in R [54]. Alpha-diversity was calculated based on the observed data rarefied using 50 rarefication runs for all analyses except the grasshoppers, which due to low sampled numbers were only rarefied 10 times.…”

“…Beta-diversity refers to species change between sites, yet two processes shape these changes, either species replacement or species loss [54]. To understand which of these two components of beta-diversity are driving the between-site variation seen in the PERMANOVA, we calculated beta-diversity and partitioned beta-diversity (changes due to species replacement and species loss separately) for each of the six site types for all taxa and per taxon in the BAT package [54].…”

“…To understand which of these two components of beta-diversity are driving the between-site variation seen in the PERMANOVA, we calculated beta-diversity and partitioned beta-diversity (changes due to species replacement and species loss separately) for each of the six site types for all taxa and per taxon in the BAT package [54]. This procedure calculates three forms of beta-diversity, namely: β total = total beta-diversity (both replacement and richness components combined), β repl = replacement component of this diversity (i.e.…”