generate_commonness_matrix_from_gdm {spectre}

generate_commonness_matrix_from_gdm

Description

Creates a pairwise site by site commonness matrix from estimates of species richness and Bray-Curtis dissimilarity.

Usage

generate_commonness_matrix_from_gdm(gdm_predictions, alpha_list)

Arguments

gdm_predictions

a square pairwise matrix of Bray-Curtis dissimilarity estimates between site pairs. We recommend using the gdm-package (Fitzpatrick et al. 2020) to generate this matrix

alpha_list

a vector of species richness for every site in the study area. The length of this vector must be equivalent to one of the dimensions of the gdm_predictions

Details

generate_commonness_matrix_from_gdm uses a vector of estimated species richness per site and a pairwise matrix of site by site Bray-Curtis dissimilarity (we recommend using the gdm-package (Fitzpatrick et al. 2020) to generate this matrix) to produce a matrix of the estimated species in common between site pairs (referred to as a commonness matrix). The commonness between sites is calculated using

C_{ij}=(1-\beta_{ij})(S_{i} + S_{j})/2

Where \beta_{ij} is the dissimilarity between sites, C_{ij} is the species in common between sites, and S is the number of species in each site. For more details see Mokany et al 2011.

Value

A pairwise site by site matrix of the number of species in common between each site pair, with dimensions equal to that of the provided dissimilarity matrix.

References

Mokany, K., Harwood, T.D., Overton, J.M., Barker, G.M., & Ferrier, S. (2011). Combining \alpha and \beta diversity models to fill gaps in our knowledge of biodiversity. Ecology Letters, 14(10), 1043-1051.