Berger-Parker's diversity index

Computes Berger-Parker's diversity index on different classes of numeric matrices using a moving window algorithm.

Usage

BergerParker(
  x,
  window = 3,
  rasterOut = TRUE,
  np = 1,
  na.tolerance = 1,
  cluster.type = "SOCK",
  debugging = FALSE
)

Arguments

x

Input data may be a matrix, a Spatial Grid Data Frame, a SpatRaster, or a list of these objects. In the latter case, only the first element of the list will be considered.

window

The side of the square moving window, it must be an odd numeric value greater than 1 to ensure that the target pixel is in the centre of the moving window. Default value is 3.

rasterOut

Boolean, if TRUE, output will be in SpatRaster format with x as a template.

np

The number of processes (cores) which will be spawned. Default value is 1.

na.tolerance

A numeric value (0.0-1.0) which indicates the proportion of NA values that will be tolerated to calculate Berger-Parker's index in each moving window over x. If the relative proportion of NA's in a moving window is bigger than na.tolerance, then the value of the window will be set as NA, otherwise, Rao's index will be calculated considering the non-NA values. Default values are 1.0 (i.e., no tolerance for NA's).

cluster.type

The type of cluster which will be created. The options are "MPI" (calls "makeMPIcluster"), "FORK", and "SOCK" (call "makeCluster"). Default type is "SOCK".

debugging

A boolean variable set to FALSE by default. If TRUE, additional messages will be printed. For de-bugging only.

Value

A numerical matrix with dimensions as dim(x).

Details

Berger-Parker's index is the relative abundance of the most abundant category (i.e., unique numerical values in the considered numerical matrix). Berger-Parker's index equals the logarithm of the inverse Renyi's index of order infinity, \(log(1/{}^\infty H)\) or the inverse of Hill's index of order infinity, \(1/{}^\infty D\).

Note

Linux users need to install libopenmpi for MPI parallel computing. Linux Ubuntu users may try: apt-get update; apt-get upgrade; apt-get install mpi; apt-get install libopenmpi-dev; apt-get install r-cran-rmpi

Microsoft Windows users may need some additional work to use "MPI", see:
https://bioinfomagician.wordpress.com/2013/11/18/installing-rmpi-mpi-for-r-on-mac-and-windows/

References

Berger, W.H., Parker, F.L. (1970). Diversity of planktonic foraminifera in deep-sea sediments". Science, 168: 1345-1347.

Author

Marcantonio Matteo marcantoniomatteo@gmail.com, Martina Iannacito martina.iannacito@inria.fr, Duccio Rocchini duccio.rocchini@unibo.it

Examples

if (FALSE) {
# Minimal example; compute Renyi's index with alpha 1:5 
a <- matrix(c(10,10,10,20,20,20,20,30,30),ncol=3,nrow=3)
berpar <- BergerParker(x=a, window=3)
}