DarkDiv: Estimating Dark Diversity and Site-Specific Species Pools
Estimation of dark diversity and site-specific species pools using species co-occurrences.
It includes implementations of probabilistic dark diversity based on the
Hypergeometric distribution, as well as estimations based on the Beals index,
which can be transformed to binary predictions using different thresholds,
or transformed into a favorability index. All methods include the possibility of
using a calibration dataset that is used to estimate the indication matrix
between pairs of species, or to estimate dark diversity directly on a single
dataset. See De Caceres and Legendre (2008) <doi:10.1007/s00442-008-1017-y>,
Lewis et al. (2016) <doi:10.1111/2041-210X.12443>,
Partel et al. (2011) <doi:10.1016/j.tree.2010.12.004>, Real et al. (2017) <doi:10.1093/sysbio/syw072>
for further information.
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