dropspc: Dropping Species with Few Occurrences

Description Usage Arguments Details Value Note Author(s) Examples

Description

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

Usage

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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 droberts@montana.edu http://ecology.msu.montana.edu/droberts/droberts.html

Examples

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

Example output

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-33. For overview type 'help("mgcv-package")'.
This is labdsv 2.0-1
convert existing ordinations with as.dsvord()

Attaching package:labdsvThe following object is masked frompackage:stats:

    density

labdsv documentation built on Aug. 4, 2019, 5:03 p.m.

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