AMBI_species: Returns species list for AMBI calculations

In ambiR: Calculate AZTI’s Marine Biotic Index

Returns species list for AMBI calculations

Description

AMBI_species() returns a dataframe with list of species and AMBI group. Called by the function AMBI() and then used to match species in observed data and find species groups.

latest version 8th October 2024

Usage

AMBI_species(version = "")

Arguments

version

string, version of the species list to return. The default value is the empty string ("") which returns the latest version of the list (8. October 2024). Currently, the only other valid value for version is "2022" (31. May 2022).

Details

The species groups, as described by Borja et al. (2000):

• Group I
  Species very sensitive to organic enrichment and present under unpolluted conditions (initial state). They include the specialist carnivores and some deposit-feeding tubicolous polychaetes.
  

• Group II
  Species indifferent to enrichment, always present in low densities with non-significant variations with time (from initial state, to slight unbalance). These include suspension feeders, less selective carnivores and scavengers.
  

• Group III
  Species tolerant to excess organic matter enrichment. These species may occur under normal conditions, but their populations are stimulated by organic enrichment (slight unbalance situations). They are surface deposit-feeding species, such as tubicolous spionids.
  

• Group IV
  Second-order opportunistic species (slight to pronounced unbalanced situations). Mainly small sized polychaetes: subsurface deposit-feeders, such as cirratulids.
  

• Group V
  First-order opportunistic species (pronounced unbalanced situations). These are deposit-feeders, which proliferate in reduced sediments.
  

Value

A data frame with 11,952 rows* and 3 columns:

species

Species name or genus (spp.)

group

Species group for AMBI index calculation: 1, 2, 3, 4 or 5. A value of 0 indicates that the species is not assigned to a species group.

RA

reallocatable (0 or 1), a 1 indicates that a species could be re-assigned to a different species group.

References

Borja, Á., Franco, J., Pérez, V. (2000). “A Marine Biotic Index to Establish the Ecological Quality of Soft-Bottom Benthos Within European Estuarine and Coastal Environments.” Marine Pollution Bulletin 40 (12): 1100–1114. \Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.1016/S0025-326X(00)00061-8")}.

See Also

AMBI() which uses the species list to calculate the AMBI index.

Examples

AMBI_species() %>% head()

AMBI_species() %>% tail()

ambiR documentation built on Dec. 20, 2025, 1:06 a.m.