rndcomm: Randomize a Community Data.Frame

In labdsv: Ordination and Multivariate Analysis for Ecology

Randomize a Community Data.Frame

Description

Permutes a vegetation (or other) data.frame to establish a basis for null model tests in vegetation ecology.

Usage

rndcomm(comm,replace=FALSE,species=FALSE,plots=FALSE)

Arguments

comm	the vegetation (or other taxon) data.frame, samples as rows, species as columns
replace	a switch for permuting (if FALSE) or boostrapping (if TRUE)
species	a switch to control randomizing by species (if TRUE), maintaining species occurrence distributions
plots	a switch to control randomizing by samples (if TRUE), maintaining plot-level species richness

Details

Permutes or bootstraps a vegetation data frame for input to dist, vegdist, dsvdis, or other routines. Can randomize by columns (species=TRUE), samples (plots=TRUE), or fully (neither species nor plots = TRUE).

Value

a data.frame with samples as rows and species as columns of the same dimensions as entered.

Note

Randomizing vegetation often leads to unrealistic data distributions, but this function attempts to preserve either species occurrence distributions or plot-level species richness. It is probably worth examining the output of this function with abuocc to see its characteristics before engaging in extensive analysis.

Author(s)

David W. Roberts [e-mail]

Examples

data(bryceveg) # returns a vegetation data.frame called bryceveg
test <- rndcomm(bryceveg,species=TRUE) # preserves species abundance
                                       # distribution
test2 <- rndcomm(bryceveg,plots=TRUE) # preserves plot-level 
                                      # species richness

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