solve_ambiguous: Methods to deal with ambiguous taxa

In alexology/biomonitoR: biomonitoring indices and metrics

Methods to deal with ambiguous taxa

Description

Solve the ambiguous assignment of taxa.

Usage

solve_ambiguous(x, method = "MCWP")

Arguments

x	Result of aggregate_taxa().
method	Only methods RPKC and MCWP are currently implemented in biomonitoR. See details.

Details

Taxonomic dataset often contains ambiguous taxa due to the difficulites in identify damaged and juvenile organisms. For instance Chironominae and Chironomidae could be reported in the same sample. Several techniques has been proposed to solve this issue (see Cuffney et al., 2007). Currently solve_ambiguous() provides two algorithms to solve the problem of ambiguous assignments. RPKC means Remove Parents - Keep Children. It works by removing all the higher taxonomic levels while keeping children. MCWP means Merge Children with Parents. It works by assignign the abundances of lower taxonomic levels to those of the higher taxonomic level.

References

Cuffney, T. F., Bilger, M. D., & Haigler, A. M. (2007). Ambiguous taxa: effects on the characterization and interpretation of invertebrate assemblages. Journal of the North American Benthological Society, 26(2), 286-307.

See Also

aggregate_taxa

Examples

data(macro_ex)
data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)
data_mcwp <- solve_ambiguous(data_agr, method = "MCWP")
data_mcwp_bio <- as_biomonitor(data_mcwp)
data_mcwp <- aggregate_taxa(data_mcwp_bio)

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