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EcoSimR (version 0.1.0)

c_score: CScore Co-occurrence Metric

Description

Takes a binary presence-absence matrix and returns Stone and Roberts' (1990) C-score.

Usage

c_score(m = matrix(rbinom(100, 1, 0.5), nrow = 10))

Arguments

m
a binary presence-absence matrix in which rows are species and columns are sites.

Value

Returns the average C-score calculated across all possible species pairs in the matrix.

Details

For each unique pair of species, the C-score is calculated as

$$C_{ij} = (R_i - S)(R_j - S)$$

where R_i and R_j are the row sums for species i and j, and S is the number of shared sites in which both species i and species j are present. For any particular species pair, the larger the C-score, the more segregated the pair, with fewer shared sites. However, the index can be difficult to interpret when calculated as a matrix-wide average, because a single matrix can contain individual pairs of species that are segregated, random, or aggregated.

Degenerate matrices result from simulations where a row or column sum may be 0.

References

Stone. L. and A. Roberts. 1990. The checkerboard score and species distributions. Oecologia 85: 74-79.

Gotelli, N.J. and W. Ulrich. 2010. The empirical Bayes approach as a tool to identify non-random species associations. Oecologia 162:463-477.

Examples

Run this code
obsCScore <- c_score(m=matrix(rbinom(100,1,0.5),nrow=10))

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