generate_commonness_matrix_from_gdm
Source:R/generate_commonness_matrix_from_gdm.R
generate_commonness_matrix_from_gdm.RdCreates a pairwise site by site commonness matrix from estimates of species richness and Bray-Curtis dissimilarity.
Arguments
- gdm_predictions
a square pairwise
matrixof Bray-Curtis dissimilarity estimates between site pairs. We recommend using the gdm-package (Fitzpatrick et al. 2020) to generate this matrix- alpha_list
a
vectorof species richness for every site in the study area. The length of this vector must be equivalent to one of the dimensions of thegdm_predictions
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.
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.