get.taxonomic: Merge benthic count data with the ITIS taxonomy table

In bio.infer: Predict Environmental Conditions from Biological Observations

Description

get.taxonomic merges the taxon names provided in a benthic count data file with a standardized taxonomy table. The purpose of this function is to provide the complete taxonomic hierarchy for each taxon.

Usage

get.taxonomic(bcnt)

Arguments

bcnt

A benthic count data frame with the following three fields: a sample identifier, taxon name, and abundance. The three fields must be ordered as listed. Sample identifier is typically a character string that is a unique identifier for a given sample. Taxon name is a character string that specifies the name of the taxon observed in the sample, and abundance is the number of individuals of that taxon that were observed.

Details

get.taxonomic attempts to match taxon names provided in a benthic count data file with taxa listed in ITIS. The script automatically corrects for the most common conventions in taxonomic naming. For example, taxon names are converted to all capital letters, and trailing strings such as "SP." and "SPP." are deleted.

The script lists taxa remaining that are not matched to entries in the ITIS database using fix. The user can then enter a corrected spelling for the taxon name.

The script provides a final summary of the unmatched taxon names, and the user can continue revising names, or complete the program.

Value

A final taxonomic table is returned as tab-delimited text in the file sum.tax.table.txt. This file is best viewed using a spreadsheet. Within R, the script returns a benthic count file with the original taxon name associated with a full taxonomic hierarchy for that taxon. The assigned species names can be modified by hand in sum.tax.table.txt and the revised information loaded with load.revised.species.

Author(s)

Lester L. Yuan

See Also

itis.ttable

Examples

data(bcnt.OR)
data(itis.ttable)
## Not run: 
bcnt.tax.OR <- get.taxonomic(bcnt.OR)

## End(Not run)

bio.infer documentation built on Sept. 2, 2020, 5:08 p.m.