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benthos (version 1.3-9)

Marine Benthic Ecosystem Analysis

Description

Preprocessing tools and biodiversity measures (species abundance, species richness, population heterogeneity and sensitivity) for analysing marine benthic data. See Van Loon et al. (2015) for an application of these tools.

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Version

Install

install.packages('benthos')

Monthly Downloads

289

Version

1.3-9

License

GPL (>= 3)

Maintainer

Dennis Walvoort

Last Published

July 4th, 2025

Functions in benthos (1.3-9)

genus_to_species

Genus to Species Conversion
get_ambi

Get Supplementary AMBI Sensitivity Groups
simpson

Simpson's Measure of Concentration
total_abundance

Total Abundance
species_richness

Species Richness
rygg

Rygg's Index of Diversity
pool

Pooling
oosterschelde

Oosterschelde Marine Benthos Data
shannon

Shannon's Index or Entropy
iti

Infaunal Trophic Index (ITI)
read_twn

Read and Validate Taxa Waterbeheer Nederland (TWN) Data
is_binomen

Binomial Names is_binomial tests for valid binomial names, generic_name extracts the genus to which the species belongs, specific_name extracts the species within the genus.
read_taxa

Read and Validate Taxa Data
strip_spaces

Remove Redundant Spaces
read_iti

Read and Validate Infaunal Trophic Index Files
to_worms

Convert Taxon Names to Comply with WoRMS
read_ref

Read and Validate Habitat References Files
hpie

Hurlbert's Probability of Interspecific Encounter (PIE)
read_ambi

Read and Validate AMBI Sensitivity Data
read_beqi2

Read and Validate BEQI2 Input Files
as_accepted

Convert Taxon Names to Comply with WoRMS/TWN
abundance

Abundance
benthos-package

Marine Benthic Ecosystem Analysis
eqr

Ecological Quality Ratio (EQR)
get_iti

Get Infaunal Trophic Index
harmonize

Harmonize Case
margalef

Margalef Index of Diversity
northsea

MWTL North Sea Bentos Data
bray_curtis

Bray-Curtis Dissimilarity
ambi

AZTI Marine Biotic Index (AMBI)
is_azoic

Test for Azoic Samples
hurlbert

Hurlbert's Expected Number of Species
hill

Hill's Diversity Numbers