ept_rich_no_tol: EPT Richness Excluding Tolerant Taxa

Description Usage Arguments Value

View source: R/diversity_metrics.R

Description

EPT Richness Excluding Tolerant Taxa

Usage

1
ept_rich_no_tol(long, rank = "FAMILY", master, tolerance_value = "BIBI_TV")

Arguments

long

Taxonomic counts arrange in a long data format (i.e., each row represents a unique sample and taxon).

rank

The taxonomic rank used to perform the analysis. You must sepecify either 'FAMILY' or "GENUS.'

master

A master taxa list including taxonomic ranks Phylum through the specified taxonomic rank (Family or Genus) and the an associated list of tolerance values. The default is set to the master taxa list included in the BIBI package. The master taxa list can be viewed with the following script: master.df <- data(master)

tolerance_value

The name of the column in the master taxon list (specified using the master variable) that contains tolerance values on a scale of 0-10. Tolerant organisms are classified as organisms with a tolerance value >= 7. The defualt is set to the the BIBI tolerance values, which are tolerance values summarized from multiple sources.

Value

The number of taxa identified as EPT (Orders: Ephemeroptera, Plecoptera, and Trichoptera), excluding taxa with a tolerance value >= 7.


zsmith27/Benthos documentation built on June 23, 2017, 12:07 p.m.