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Calculate community metrics (version 0.0.2)
Observation data file, with location, year, species and abundance.
Presence/absence, Species richness, Simpson and Shannon index are systematically computed.

Calculate community metrics from abundance data

What it does

This tool from PAMPA toolsuite computes community metrics from abundance data:

  • Species richness / alpha diversity
  • Shannon index
  • Simpson index
  • Pielou index
  • Hill index

Input description

A tabular file with observation data. Must at least contain three columns 'observation.unit' which associate year and location or 'year' and 'location', 'species.code' with species ID and 'number' for abundance.

observation.unit species.code number
site_yearID speciesID 4
... ... ...

OR

year location species.code number
2000 locationID speciesID 4
... ... ... ...

The data frame may also contain:

  • 'size.class' field with 'G' representing big individuals in given species, 'M' middle-sized individuals and 'P' small individuals
  • 'rotation' field for STAVIRO data

Output

A tabular file with every metrics selected computed per observation unit


Source

Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.