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Parallel Computation of Renyi's Diversity Index

Source: R/RenyiP.R
RenyiP.Rd

This function computes Renyi's diversity index for each cell of a matrix, using a parallelized approach and considering a specified moving window.

Usage

RenyiP(
  x,
  window = 1,
  alpha = 1,
  base = exp(1),
  na.tolerance = 1,
  debugging = FALSE,
  np = 1
)

Arguments

x

A numeric matrix representing the data on which the index is to be calculated.

window

The width of the moving window to consider for each cell. The actual window size will be `(2 * window + 1) x (2 * window + 1)`. Default is 1.

alpha

The alpha parameter for Renyi's index, influencing sensitivity to species abundance. Default is 1.

base

The base of the logarithm used in Renyi's formula. Default is `exp(1)` (natural logarithm).

na.tolerance

The tolerance level for missing data within the moving window. A window will be processed only if the proportion of non-missing data is above this threshold. Value should be between 0 and 1. Default is 1.

debugging

Boolean flag to enable or disable debugging messages. Default is FALSE.

np

Number of processes for parallel computation.#'

Value

A matrix of the same dimensions as `x`, where each cell contains the Renyi's diversity index calculated for the window around the cell.

Examples

data <- matrix(runif(100), nrow = 10)
renyi_index <- RenyiP(data, window = 1, np = 1)
#> 
#> 
#> Processing alpha: 1 Moving Window: 3
#> Warning: executing %dopar% sequentially: no parallel backend registered
#> 
#> 
#>  Parallel calculation of Renyi's index complete.