Marine Benthic Ecosystem Analysis

---

Documentation for package ‘benthos’ version 1.3-8

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

benthos-package	Marine Benthic Ecosystem Analysis
.pool	Pooling
abundance	Abundance
abundance_	Abundance
ambi	AZTI Marine Biotic Index (AMBI)
ambi_	AZTI Marine Biotic Index (AMBI)
as_accepted	Convert Taxon Names to Comply with WoRMS/TWN
benthos	Marine Benthic Ecosystem Analysis
bray_curtis	Bray-Curtis Dissimilarity
eqr	Ecological Quality Ratio (EQR)
generic_name	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.
genus_to_species	Genus to Species Conversion
get_ambi	Get Supplementary AMBI Sensitivity Groups
get_iti	Get Infaunal Trophic Index
get_taxa	Read and Validate Taxa Data
get_worms	Read and Validate Taxa Waterbeheer Nederland (TWN) Data
harmonize	Harmonize Case
has_ambi	AZTI Marine Biotic Index (AMBI)
has_ambi_	AZTI Marine Biotic Index (AMBI)
has_iti	Infaunal Trophic Index (ITI)
has_iti_	Infaunal Trophic Index (ITI)
hill	Hill's Diversity Numbers
hill0	Hill's Diversity Numbers
hill0_	Hill's Diversity Numbers
hill1	Hill's Diversity Numbers
hill1_	Hill's Diversity Numbers
hill2	Hill's Diversity Numbers
hill2_	Hill's Diversity Numbers
hill_	Hill's Diversity Numbers
hpie	Hurlbert's Probability of Interspecific Encounter (PIE)
hpie_	Hurlbert's Probability of Interspecific Encounter (PIE)
hurlbert	Hurlbert's Expected Number of Species
hurlbert_	Hurlbert's Expected Number of Species
is_accepted	Convert Taxon Names to Comply with WoRMS
is_accepted_	Convert Taxon Names to Comply with WoRMS
is_azoic	Test for Azoic Samples
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.
is_worms	Convert Taxon Names to Comply with WoRMS
is_worms_	Convert Taxon Names to Comply with WoRMS
iti	Infaunal Trophic Index (ITI)
iti_	Infaunal Trophic Index (ITI)
lnn	Total Abundance
lnn_	Total Abundance
margalef	Margalef Index of Diversity
margalef_	Margalef Index of Diversity
northsea	MWTL North Sea Bentos Data
oosterschelde	Oosterschelde Marine Benthos Data
pool	Pooling
read_ambi	Read and Validate AMBI Sensitivity Data
read_beqi2	Read and Validate BEQI2 Input Files
read_iti	Read and Validate Infaunal Trophic Index Files
read_ref	Read and Validate Habitat References Files
read_taxa	Read and Validate Taxa Data
read_twn	Read and Validate Taxa Waterbeheer Nederland (TWN) Data
rygg	Rygg's Index of Diversity
rygg_	Rygg's Index of Diversity
shannon	Shannon's Index or Entropy
shannon_	Shannon's Index or Entropy
simpson	Simpson's Measure of Concentration
simpson_	Simpson's Measure of Concentration
species_richness	Species Richness
species_richness_	Species Richness
specific_name	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.
strip_sp	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.
strip_spaces	Remove Redundant Spaces
total_abundance	Total Abundance
total_abundance_	Total Abundance
to_worms	Convert Taxon Names to Comply with WoRMS
validate_ambi	Read and Validate AMBI Sensitivity Data
validate_beqi2	Read and Validate BEQI2 Input Files
validate_iti	Read and Validate Infaunal Trophic Index Files
validate_ref	Read and Validate Habitat References Files
validate_taxa	Read and Validate Taxa Data
validate_twn	Read and Validate Taxa Waterbeheer Nederland (TWN) Data