ibmr: Biologique Macrofitique en Riviere index

In alexology/biomonitoR: biomonitoring indices and metrics

Biologique Macrofitique en Riviere index

Description

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

This function calculates the IBMR index following Minciardi et al. (2009).

Usage

ibmr(
  x,
  method = "ita",
  exceptions = NULL,
  coverage_coef = FALSE,
  coverage_classes = c(0.1, 1, 10, 50),
  traceB = FALSE
)

Arguments

x	Result of aggregate_taxa().
method	The implementation of IBMR. the default method is ita (Minciardi et al., 2009). Users can provide their own data.frame (see examples) with a column called Taxon and the column of scores called Scores.
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.
coverage_coef	Are data already represented with coverage coefficients? Set to TRUE if this is not the case.
coverage_classes	Thresholds to transform abundances into coverage classes.
traceB	If set to TRUE a list as specified below will be returned.

Details

The function ibmr() calculates the index as follow:

ibmr= \frac{\sum_{i=1}^{S} C{i} E{i} K{i}} {\sum_{i=1}^{S} E{i} K{i}}

where S is the number of taxa, i the ith taxon, Ci the sensitivity score, Ei the stenoecia coefficient and Ki the coverage coefficient.

Be careful when using data already transformed in coverage classes. The function ibmr() will sum the classes if needed and this will result in wrong results. For example, if a taxon has only genus level scores and two species of this genus are present, ibmr() will sum their coverage classes. This can result in taxa having a coverage class higher than the highest coverage class allowed.

All the information used for ibmr() 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.

• 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

Minciardi, M. R., Spada, C. D., Rossi, G. L., Angius, R., Orru, G., Mancini, L., Pace, G., Marcheggiani, S., Puccinelli, C. (2009). Metodo per la valutazione e la classificazione dei corsi d'acqua utilizzando la comunita delle macrofite acquatiche. ENEA Rapporto Tecnico RT/2009/23/ENEA.

See Also

aggregate_taxa

Examples

data(oglio)
oglio_asb <- as_biomonitor(oglio, group = "mf", FUN = bin)
oglio_agg <- aggregate_taxa(oglio_asb)
ibmr(oglio_agg)

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