bioco: biocontamination index

In alexology/biomonitoR: biomonitoring indices and metrics

biocontamination index

Description

This function provides site-specific biocontamination index (SBCI), abundance contamination index (ACI) and richness contamination index (RCI) at family rank according to by Arbaciauskas et al. (2008).

Usage

bioco(x, alien = NULL, dfref = NULL, digits = 2)

Arguments

x	Result of aggregate_taxa().
alien	A vector containing the alien taxa name. Only taxa up to family level will be considered.
dfref	Reference dataset. If a default reference dataset is used, use mi for macroinvertebrates, mf for macrophytes and fi for fish. Use the same reference dataset you used for as_biomonitor() otherwise.
digits	Number of decimal places, default to 2 as in the original work of Arbaciauskas et al. (2008).

Details

Biocontamination of sampling sites can be assessed using a site-specific biocontamination index (SBCI) derived from two metrics: abundance contamination index (ACI) and richness contamination index (RCI) at family/ordinal rank. These indices are calculated as:

ACI = Na/Nt

where Na and Nt are numbers of specimens of alien taxa and total specimens in a sample, respectively, and

RCI = Ta/Tt

where Ta is the total number of alien families/orders, and Tt is the total number of identified families/orders. With values of ACI and RCI, the site-specific biocontamination index (SBCI) can then be derived from an easy double entry matrix (Arbaciauskas et al. 2008). Five classes of biocontamination ranging from 0 ("no" contamination) to 4 ("severe" contamination) are defined. A global alien species dataset cannot be provided because alien species may vary among different biogeographical regions and countries. For this reason users need to define and properly upload their own alien reference database. Applications and examples of these indices are available in Cuk et al. (2019) for Croatian rivers, Guareschi et al. (2021) for UK rivers and MacNeil et al. (2010) (The Isle of Man).

References

Arbaciauskas, K., Semenchenko, V., Grabowski, M., Leuven, R.S.E.W., Paunovic, M., Son, M.O., Csanyi, B., Gumuliauskaite, S., Konopacka, A., Nehring, S., Van der Velde, G., Vezhnovetz, V., Panov, V.E. (2008). Assessment of biocontamination of benthic macroinvertebrate communities in European inland waterways. Aquatic Invasions 3 (2): 211-230.

Cuk, R., Milisa, M., Atanackovic, A., Dekic, S., Blazekovic, L., & Zganec, K. (2019). Biocontamination of benthic macroinvertebrate assemblages in Croatian major rivers and effects on ecological quality assessment. Knowledge & Management of Aquatic Ecosystems, (420), 11.

MacNeil, C., Briffa, M., Leuven, R.S., Gell, F.R. and Selman, R. (2010). An appraisal of a biocontamination assessment method for freshwater macroinvertebrate assemblages; a practical way to measure a significant biological pressure? Hydrobiologia 638:151-159

Guareschi, S., Laini, A., England, J., Barrett, J. and Wood, P.J., (2021). Multiple co-occurrent alien invaders constrain aquatic biodiversity in rivers. Ecological Applications, p.e2385.

See Also

aggregate_taxa

Examples

data(macro_ex)
data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)
# Toy example:
alien <- c("Laccobius", "Setodes bulgaricus", "Caenidae")
bioco(data_agr, alien = alien, dfref = "mi")

alexology/biomonitoR documentation built on Oct. 10, 2024, 12:02 a.m.