Simulated 100-cell box subsampler

sub.sample {sub.sample}

Description

Produces simulated random subsamples of species counts in a sample-by-species matrix

Usage

sub.sample(x, fixed.percentage = FALSE, min.count = TRUE, count = 300,
tolerance = 5, min.percentage = FALSE, percentage = 10, max.percentage = 90)

Arguments

`x`	a data frame with samples in columns and taxa in rows
`fixed.percentage`	if TRUE, all columns are subsampled by a fixed percentage, as defined by `percentage`. (Overrides min.count and min.percentage)
`min.count`	if TRUE, each subsample contains a minimum number of individuals as defined by `count`.
`count`	the minimum number of individuals in each subsample
`tolerance`	the number of individuals less than `count` that constitutes an acceptable subsample
`min.percentage`	if TRUE, each subsample is at least a minimum percentage as defined by `percentage`
`percentage`	the minimum percentage subsample size
`max.percentage`	percentage subsample beyond which the subsampling effort outweighs the effort of sorting the whole sample: therefore, whole sample taken

Details

This function simulates a 100-cell box subsampler as described by Marchant (1989). For a fixed-count subsample, it makes a first attempt at subsampling by calculating the number of cells on average to collect the required number. If the number collected is less than the required number (minus the tolerance level), then further one-percent subsamples are taken until the number is exceeded.

Value

a list containing

`subsampled.set`	a data frame of the same structure of x, but with subsampled counts
`subsample.size`	a vector of proportional subsample sizes for each column
`number.in.subsample`	a vector of the total number of individuals in each subsampled column

Author(s)

Chris Walsh: Chris.Walsh@sci.monash.edu.au.

References

Marchant, R. (1989) A subsampler for samples of benthic invertebrates. Bulletin of the Australian Society for Limnology 12, 49-52.

Examples

urban <- read.table("urban.txt", header=TRUE) urban.10perc <- sub.sample(urban[,2:24], fixed.percentage = TRUE, percentage = 10) urban.10perc #Fixed 10 percent subsamples urban.300count <- sub.sample(urban[,2:24]) urban.300count #Fixed count subsamples of 300 individuals urban.300or10 <- sub.sample(urban[,2:24], min.percentage = TRUE) urban.300or10 #Fixed count of 300 individuals, conditional on subsample #being at least 10 percent.

Urban Water Ecology