get.otu: Defines operational taxonomic units (OTUs)

Description

get.otu generates OTUs for benthic count data using a simple algorithm that is designed to maximize the amount of taxonomic information retained across the entire data set, while eliminating redundant taxonomic identifications.

Usage

get.otu(bcnt, optlist = NULL, ndc = TRUE, outputFile = FALSE,
gui = FALSE)

Arguments

bcnt

benthic count data frame that includes the full taxonomic hierarchy for each taxon. Typically, bcnt is the output from get.taxonomic.

optlist

vector of taxon names for which trait or tolerance value is available. Specify optlist = NULL for cases in which OTU are computed without regard for any additional taxon specific information, e.g. for developing a RIVPACS model.

ndc

Logical flag indicating whether OTU should be computed that eliminate double-counting of taxa.

outputFile

Logical indicating whether to output summary information

gui

Logical indicating whether to use gui interface.

Value

Final OTU decisions are returned as tab-delimited text file, sum.otu.txt, which is best viewed using a spreadsheet. A new benthic count file is also returned in R, including the original benthic count information and a new field specifying the OTU designation for each taxon. Manual revisions to the assigned OTUs can be recorded in sum.otu.txt and loaded with load.revised.otu

Details

get.otu makes decisions about OTU according to the following rule. The number samples in which a given taxonomic group (e.g. Baetidae) is observed, is compared to the number of samples in which members of the that same group are identified to a higher taxonomic level (e.g., Baetis, Fallceon, Acentrella, etc.). If more samples are observed with the coarser identification, then all identifications are downgraded to the coarse identification. If more samples are observed at the finer level of identification, then those sample are retained, and all identifications at the coarser level are omitted. Before deciding on OTU assignments, the script first reviews the species names that are listed in the benthic count file and matches them with the species names provided in optlist.

Examples

Run this code

# NOT RUN {
data(bcnt.tax.OR)
data(coef.west.wt)
bcnt.otu.OR <- get.otu(bcnt.tax.OR, coef.west.wt)
# }