Beals smoothing R functions

Introduction: Beals smoothing is a multivariate transformation specially designed for species presence/absence community data containing noise and/or a lot of zeros. This transformation replaces the observed values of the target species by predictions of occurrence on the basis of its co-occurrences with the remaining species. In many applications, the transformed values are used as input for multivariate analyses. As Beals smoothing values provide a sense of ‘‘probability of occurrence’’, they have also been used for inference. However, this transformation can produce spurious results, and it must be used with caution. We include here a set of functions to conduct the transformation and to test its validity.

Authors: Miquel De Cáceres, Jari Oksanen

Availability: Uncompress the following ZIP file. Includes an R script file and a user manual in PDF.

Beals smoothing functions included (see also function ‘beals’ in package vegan)

  • beals()
  • beals.sp()
  • BSS.test()