Introduction

This module estimates environmental conditions from observations of benthic macroinvertebrates for a set of sites, by combining observations of each particular taxon with a taxon-environment relationship. This calculation has three steps. First, observations of benthic macroinvertebrates are matched with standard taxonomic names, with a full taxonomic hierarchy. Second, operational taxonomic units (OTUs) are defined for the data set, so that each individual taxon is counted at a consistent taxonomic level. Third, observations are matched with existing taxon-environment relationships and an estimate of environmental conditions computed.

The module is initiated by choosing Analysis Tools -> Predicting env. conditions from biological observations from the menus. A dialog box should appear as follows:

Input files

Active Dataset: This file is a data frame that contains observations of benthic macroinvertebrate. The file can be selected from the working directory or loaded using the Browse option. At least three columns are required in this data frame: (1) a unique sample identifier (specified by selecting the appropriate field in Site ID:, (2) taxon names (specified in Taxon Name, and (3) the number of individuals of a particular taxon within a particular sample (Taxon Count).

Coefficient data: Select a coefficient file that represent taxon-environment relationships from those available in bio.infer. Two coefficient files are currently available: temperature and sediment relationships in the western U.S. (coef.west.wt) and sediment relationships in the eastern U.S. (coef.east.sed). Alternatively, a user generated coefficient file (using the bio.infer script taxon.env) can be loaded.

Output file

Results: Select this option to save the results of the script in a separate text file.