bio.infer-package {bio.infer}

Scripts for computing biological inferences

Description

Reformats raw benthic count files, combines them with existing taxon-environment relationships, and computes inferences of environmental conditions.

Details

Package:	bio.infer
Type:	Package
Version:	1.0
Date:	2006-10-31
License:	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 bcnt.OR for an example of the required format). This benthic count file will be merged with standardized taxonomic hierarchy information using get.taxonomic. 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 preferences.)

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 (mlsolve).

This package was developed in Windows but should be fully functional in other operating systems.

Author(s)

Lester L. Yuan