bidensity: Rescaled bipartite density (BC) of Sidor et al. 2013

In adamkocsis/obigeo: Occurrence-based biogeography

Rescaled bipartite density (BC) of Sidor et al. 2013

Description

The proportion of manifested connections out of all potential connections.

Usage

bidensity(dat, tax, loc, bin = NULL)

Arguments

dat	(data.frame) Occurrence dataset.
tax	(character) Column name of taxon entries
loc	(character) Column name of locality/cell entries.
bin	(character) Column name of bin ids. Optional, if the function is to be iterated for multiple bins.

Details

The variables is called BC in Sidor et al. 2013 and is caclulated as: BC = (O-N)/LN-N'

"where O is the number of links in the occurrence network (number of occurrences), N is the number of taxa, and L is the number of localities. The numerator is the number of occurrences of taxa beyond a single locality (hence why N is subtracted from O), and the denominator is the number of occurrences that could conceivably occur (LN), minus one occurrence for each species because each species must occur at least once. This measure is bounded between 0 (when O = N) and 1 (when O = LN), which correspond to extreme occurrence network topologies of minimum and maximum homogeneity"

Sidor, C. A., D. A. Vilhena, K. D. Angielczyk, A. K. Huttenlocker, S. J. Nesbitt, B. R. Peecook, J. S. Steyer, R. M. H. Smith, and L. A. Tsuji. 2013: Provincialization of terrestrial faunas following the end-Permian mass extinction. Proceedings of the National Academy of Sciences 110:8129-8133.

Examples

data(ceno6)
bidensity(ceno6, tax="trinomen", loc="icos", bin="stg")

adamkocsis/obigeo documentation built on Oct. 14, 2024, 8:46 a.m.