BergerParker: Berger-Parker's diversity index
In rasterdiv: Diversity Indices for Numerical Matrices

BergerParker

R Documentation

Berger-Parker's diversity index

Description

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.

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.

Value

A numerical matrix with dimensions as dim(x).

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/

Author(s)

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

References

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

Examples

## Not run: 
# 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)

## End(Not run)

rasterdiv documentation built on Oct. 14, 2024, 5:10 p.m.