dropspc: Dropping Species with Few Occurrences

In labdsv: Ordination and Multivariate Analysis for Ecology

Dropping Species with Few Occurrences

Description

Eliminates species from the community data frame that occur fewer than or equal to a threshold number of occurrences.

Usage

dropspc(comm,minocc=0,minabu=0)

Arguments

comm	a community data frame
minocc	the threshold number of occurrences to be dropped
minabu	the threshold minimum abundance to be dropped

Details

The function is useful for eliminating species (columns) from community data frames which never occur, which often happens if you eliminate plots, and those plots are the only ones that contain that species. In addition, many species are rare in data frames, and some algorithms (especially dissimilarity functions and table sorting routines) benefit from smaller, simpler data frames.

Value

Produces a new community data frame

Note

This is a heavy-handed approach to managing rare species in data.frames. It is often possible to write a mask (logical vector) that suppresses the influence of rare species and keeps the original data.frame intact, but this function simplifies data management for some purposes.

Author(s)

David W. Roberts [e-mail]

Examples

data(bryceveg) # returns a data frame called bryceveg
newveg <- dropspc(bryceveg,5) # deletes species which 
                              # occur 5 or fewer times

labdsv documentation built on April 10, 2023, 5:08 p.m.