aspt: Average Score Per Taxon

In alexology/biomonitoR: biomonitoring indices and metrics

Average Score Per Taxon

Description

\Sexpr[results=rd, stage=render]{ lifecycle::badge("maturing") }

This function calculates the Average Score Per Taxon index following Armitage et al. (1983), Davy-Bowker et al. (2007) and Alba-Tercedor & Sanchez-Ortega (1988) implementations.

Usage

aspt(x, method = "ita", agg = FALSE, exceptions = NULL, traceB = FALSE)

Arguments

x	Result of aggregate_taxa().
method	The implementation of BMWP needed to calculate ASPT. Possible choices are a (Armitage et al. 1983), uk (Davy-Bowker et al. 2010), spa (MAGRAMA 2011), ita (Buffagni et al . 2014). Users can provide their own data.frame (see examples) with a column called Taxon and the column of scores called Scores.
agg	This option allows the composite family approach. It can be FALSE, TRUE or a data.frame. If FALSE no aggregation will be performed, while if TRUE aggregation will be performed according to the rules described in Details. A data.frame containing the aggregation rules can be provided by the user. This data.frame needs a column called Taxon containing the taxon to aggregate and a column called Correct_Taxon with the aggregation specifications. agg cannot be TRUE when a data.frame is provided as method.
exceptions	Taxa that need to be excluded from the calculation. This option can be useful, for instance, to exclude an alien species belonging to an autochthonous family.
traceB	If set to TRUE a list as specified below will be returned.

Details

ASPT is the average scores of the families that receive the score. Armitage scores are not reliable yet, since taxonomy has to be revised (e.g. Elminthidae are present instead of Elmidae). Davy-Bowker et al. (2010) and Buffagni et al. (2014) implementations take into account composite taxa as follow:

1. Psychomyiidae (inc. Ecnomidae)

2. Rhyacophilidae (inc. Glossosomatidae)

3. Limnephilidae (inc. Apatanidae)

4. Ancylidae (inc. Acroloxidae)

5. Gammaridae (inc. Crangonyctidae & Niphargidae)

6. Hydrophilidae (inc. Hydraenidae, Helophoridae)

7. Tipulidae (inc. Limoniidae, Pediciidae & Cylindrotomidae)

8. Planariidae (inc. Dugesidae)

9. Hydrobiidae (inc. Bithyniidae)

10. Oligochaeta (all the families)

Optional scores provided by the user data.frame needs to be formatted like following:

Taxon	Scores
Aeshnidae	8
Ancylidae	6
Aphelocheiridae	10
Asellidae	3
Astacidae	8

Optional aggregation data.frame provided by the user needs to be formatted like following:

Taxon	Correct_Taxon
Glossosomatidae	Rhyachopilidae
Apataniidae	Limnephilidae
Acroloxidae	Ancylidae
Crangonyctidae	Gammaridae
Niphargidae	Gammaridae

The aspt() function automatically check for parent-child pairs in the scoring system, see the Value section for a definition. All the information used for aspt() calculation can be retrieved with the function show_scores.

Value

If traceB is set to TRUE a list with the following elements will be returned:

• results Result of aspt().

• taxa_df The data.frame used for the calculation containing the abundance of taxa receiving a score.

• composite_taxa Taxa aggregated following the aggregation rules when agg is not NULL.

• exceptions A data.frame containing the changes made by excluding the taxa included in exceptions.

• parent_child_pairs For instance in Spanish ASPT both Ferrissia and Planorbidae receive a score. Abundances of the higher taxonomic level need therefore to be adjusted by subtracting the abundances of the lower taxonomic level.

References

Armitage, P. D., Moss, D., Wright, J. F., & Furse, M. T. (1983). The performance of a new biological water quality score system based on macroinvertebrates over a wide range of unpolluted running-water sites. Water research, 17(3), 333-347.

Davy-Bowker J., Clarke R., Corbin T., Vincent H, Pretty J., Hawczak A., Blackburn J., Murphy J., Jones I., 2008. River Invertebrate Classification Tool. Final report. WFD72C. SNIFFER. 276 pp

MAGRAMA-Ministerio de Agricultura y medio Ambiente (2011) Protocolo de muestreo y laboratorio de fauna bentonica de invertebrados en rios vadeables. ML-Rv-I-2011, Cod, 23 pp.

See Also

aggregate_taxa bmwp

Examples

data(macro_ex)
data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)
aspt(data_agr)
aspt(data_agr, method = "spa")

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