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benthos (version 1.3-8)

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

318

Version

1.3-8

License

GPL (>= 3)

Maintainer

Dennis Walvoort

Last Published

August 22nd, 2022

Functions in benthos (1.3-8)

as_accepted

Convert Taxon Names to Comply with WoRMS/TWN
northsea

MWTL North Sea Bentos Data
margalef

Margalef Index of Diversity
get_iti

Get Infaunal Trophic Index
benthos-package

Marine Benthic Ecosystem Analysis
harmonize

Harmonize Case
bray_curtis

Bray-Curtis Dissimilarity
hurlbert

Hurlbert's Expected Number of Species
read_taxa

Read and Validate Taxa Data
read_twn

Read and Validate Taxa Waterbeheer Nederland (TWN) Data
eqr

Ecological Quality Ratio (EQR)
read_iti

Read and Validate Infaunal Trophic Index Files
abundance

Abundance
ambi

AZTI Marine Biotic Index (AMBI)
oosterschelde

Oosterschelde Marine Benthos 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_ref

Read and Validate Habitat References Files
genus_to_species

Genus to Species Conversion
get_ambi

Get Supplementary AMBI Sensitivity Groups
hill

Hill's Diversity Numbers
pool

Pooling
rygg

Rygg's Index of Diversity
shannon

Shannon's Index or Entropy
is_azoic

Test for Azoic Samples
total_abundance

Total Abundance
hpie

Hurlbert's Probability of Interspecific Encounter (PIE)
iti

Infaunal Trophic Index (ITI)
species_richness

Species Richness
simpson

Simpson's Measure of Concentration
read_ambi

Read and Validate AMBI Sensitivity Data
read_beqi2

Read and Validate BEQI2 Input Files
strip_spaces

Remove Redundant Spaces
to_worms

Convert Taxon Names to Comply with WoRMS