allrich: Function for calculating richness at different taxonomic...

In alexology/biomonitoR: biomonitoring indices and metrics

Function for calculating richness at different taxonomic levels

Description

This function allows the calculation of richness at different taxonomic levels and of the total abundance. A convenient function for calculating richness at all the taxonomic levels simultaneously is provided.

Usage

allrich(x)

richness(x, tax_lev = "Taxa")

Arguments

x	Result of aggregate_taxa().
tax_lev	Taxonomic level at which the calculation has to be performed.

Details

richness() returns a warning meassage if unassigned taxa are detected at the desired taxonomic level. Unassigned taxa can be present because some taxa are entered at higher taxonomic levels than those at which the calculation is performed. For instance, this problem appears when the calculation is performed at genus level and some taxa has been entered at family level. Unassigned taxa can be present also because of missing levels in the reference database at the desired taxonomic level. This problem is present, for example, for Mollusca in the default database for macroinvertebrates. Mollusca orders are not present because there is no consensus among taxonomist (see the www.molluscabase.org website).

Functions

• richness: Taxonomic richness

See Also

aggregate_taxa

Examples

data(macro_ex)
data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)
richness(data_agr, tax_lev = "Family")

alexology/biomonitoR documentation built on April 7, 2024, 10:15 a.m.