dness: dness

In alexology/biomonitoR: biomonitoring indices and metrics

dness

Description

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

This function calculates the taxonomic diversity, taxonomic distinctness and variation of taxonomic distinctness.

Usage

dness(
  x,
  complete = FALSE,
  tax_lev = "Genus",
  method = "delta",
  taxa_tree = FALSE
)

Arguments

x	Result of aggregate_taxa().
complete	If TRUE unassigned taxon are removed from the taxonomic list of the desired taxonomic level set with tax_lev.
tax_lev	Taxonomic level from which the indices have to be calculated.
method	Available methods are delta (taxonomic diversity), delta.st (taxonomic distinctness) and delta.bin (variation in taxonomic distinctness).
taxa_tree	If TRUE dness() return a list where the first element is the taxonomic diversity, taxonomic distinctness or variation of taxonomic distinctness and the second elemnt the taxonomic tree

Details

These indeces take into account the taxonomic relatedness of the species in each sample. According to Clarke and Warwick (1998, 2001), taxonomic diversity is the average taxonomic ‘distance’ between any two organisms chosen at random from the sample, taxonomic distinctness is the average path length between any two randomly chosen individuals conditional on them being from different species and variation in taxonomic distinctness is the variance of the path length through the taxonomic tree connecting every pair of species in the list and reflects the unevenness of the taxonomic tree.

References

Clarke, K. R., & Warwick, R. M. (1998). A taxonomic distinctness index and its statistical properties. Journal of applied ecology, 35(4), 523-531.

Clarke, K. R., & Warwick, R. M. (2001). A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Marine ecology Progress series, 216, 265-278.

See Also

aggregatoR

Examples

data(oglio)
data_bio <- as_biomonitor(oglio, group = "mf")
data_agr <- aggregate_taxa(data_bio)
dness(data_agr, complete = TRUE)

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