eptd: eptd

In alexology/biomonitoR: biomonitoring indices and metrics

eptd

Description

This function calculates the log10(Sel_EPTD + 1) index, where EPTD stands for Ephemeroptera, Plecoptera, Trichoptera and Diptera.

Usage

eptd(x, base = 10, eptd_families = NULL, traceB = FALSE)

Arguments

x	Result of aggregate_taxa().
base	Base of the logarithm. Default to 10.
eptd_families	A vector of selected EPTD taxa at family level. Optional, default to NULL.
traceB	If set to TRUE a list as specified below will be returned.

Details

log10(Sel_EPTD + 1) is the base-10 logarithm of the abundance of the selected EPTD families plus 1. Selected EPTD families are Heptageniidae, Ephemeridae, Leptophlebiidae, Brachycentridae, Goeridae, Polycentropodidae, Limnephilidae, Odontoceridae, Dolichopodidae, Stratiomyidae, Dixidae, Empididae, Athericidae and Nemouridae. This metric is part of the italian STAR_ICMi index, where it is supposed to be relate to habitat integrity. To accomodate for other EPTD taxa, users can provide their own list of taxa as a character vector.
The function eptd() will search for the selected EPTD within Ephemeroptera, Plecoptera, Trichoptera and Diptera set at Order level. If store Ephemeroptera, Plecoptera, Trichoptera and Diptera are stored at taxonomic level other than Order, this function will not work properly, see get_taxa_abundance() instead.

Value

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

• results Results of the log10(Sel_EPTD + 1) index.

• taxa_df The data.frame used for the calculation containing the abundance of the EPTD taxa.

See Also

aggregate_taxa get_taxa_abundance

Examples

data(macro_ex)
data_bio <- as_biomonitor(macro_ex)
data_agr <- aggregate_taxa(data_bio)
eptd(data_agr)

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