rndcomm: Randomize a Community Data.Frame

Description Usage Arguments Details Value Note Author(s) Examples

View source: R/rndcomm.R

Description

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

Usage

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

Examples

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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 Aug. 4, 2019, 5:03 p.m.

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