rndtaxa {labdsv}R Documentation

Randomize a Taxa Data.Frame

Description

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

Usage

rndtaxa(taxa,replace=FALSE,species=FALSE,plots=FALSE)

Arguments

taxa 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 droberts@montana.edu

References

http://ecology.msu.montana.edu/labdsv/R/labdsv

Examples

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

[Package labdsv version 1.3-1 Index]