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Compute Rao's entropy index (Rao's Q)

Source: R/fd_raoq.R
fd_raoq.Rd

This function computes Rao's Quadratic Entropy following Rao (1982). NB: Rao's quadratic entropy is 0 when there are no species in the site.

Usage

fd_raoq(traits = NULL, sp_com, dist_matrix = NULL)

Arguments

traits

Trait matrix with species as rows and traits as columns. It has to contain exclusively numerical values. This can be either a matrix, a data.frame, or a Matrix::Matrix() object.

sp_com

Site-species matrix with sites as rows and species as columns if not provided, the function considers all species with equal abundance in a single site. This can be either a matrix, a data.frame, or a Matrix::Matrix() object.

dist_matrix

A dissimilarity matrix that can be provided instead of a trait data.frame (default: NULL). This can be either a matrix, a data.frame, or a Matrix::Matrix() object.

Value

a data.frame with two columns:

  • site the names of the sites as the row names of the input sp_com,

  • Q the values of Rao's quadratic entropy at each site.

If the sp_com argument is not provided or if sp_com doesn't have rownames, arbitrary rownames s1, s2, s3, etc. will be used.

NB: Rao's quadratic entropy is 0 when there are no species in the site.

References

Pavoine S., Dolédec S. (2005). The apportionment of quadratic entropy: a useful alternative for partitioning diversity in ecological data. Environmental and Ecological Statistics, 12(2), 125–138. doi:10.1007/s10651-005-1037-2

Examples

data(traits_birds)
fd_raoq(traits_birds)
#>   site        Q
#> 1   s1 170.0519