| benthos-package {benthos} | R Documentation |
Marine Benthic Ecosystem Analysis
Description
benthos provides functions for facilitating the analysis of marine benthos data. Examples are indicators like species abundance, species richness, Margalef's index of diversity, Shannon's Entropy, AZTI's Marine Biotic Index, and the Infaunal Trophic Index (ITI). In addition functions for data pooling, genus-to-species conversion and validation and conversion of species names to those recommended by the World Register of Marine Species are provided.
Details
All functions are designed to work seamlessly with the dplyr-package which implements a grammar for structured data manimpulation.
The benthos-package contains functions for estimating various species abundance, species richness, species heterogeneity and species sensitivity measures:
total abundance (
total_abundance)abundance (
abundance)species richness (
species_richness)Margalef's index of diversity (
margalef)Rygg's index of diversity (
rygg)Hurlbert's Expected Number of Species (
hurlbert)Simpson's measure of concentration (
simpson)Hurlbert's probability of interspecific encounter (PIE) (
hpie)Shannon's index or entropy (
shannon)Hill's diversity number (
hill)AZTI Marine Biotic Index (AMBI) (
ambi)Infaunal Trophic Index (ITI) (
iti)Bray-Curtis dissimilarity (
bray_curtis)
In addition, functions are available for data preparation, e.g.:
data pooling (
pool)genus to species conversion (
genus_to_species)
For an overview of all the functions in the package click on the index link at the bottom of this page.
Author(s)
Dennis Walvoort dennis.walvoort@wur.nl
See Also
The BEQI2-package on CRAN, and the package vignettes.