Reformats raw benthic count files, combines them with existing taxon-environment relationships, and computes inferences of environmental conditions.
|GPL version 2 or newer
Use this package to import benthic count data, reformat the data, and compute inferences of environmental conditions using taxon-environment relationships.
Typically, the user will start by loading a local benthic count
data file (see
for an example of the required format).
This benthic count file will be merged with standardized
taxonomic hierarchy information using
Then, operational taxonomic units will be assigned, based on the number
of occurrences of different taxa and based on the identity of taxa for
which environmental preferences have been quantified. (See
get.otu for the OTU assignment script, and
coef.west.wt for an example file of environmental
Once OTUs have been assigned, the benthic count file is reformatted as a
site-taxon matrix (
makess). This file can then be used to
compute biological inferences (
This package was developed in Windows but should be fully functional in other operating systems.
Lester L. Yuan
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