CADStat: Statistical Tools for Causal Analysis

Predicting environmental conditions from biological observations

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 Environmental 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. An example file, bcnt.OR.rda, can be found in the data subfolder of the package bio.infer. At least three columns are required in this data frame:

• Site ID: A unique sample identifier.
• Taxon Name: The names of taxons.
• Taxon Count: The number of individuals of a particular taxon within a particular sample.

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 Save R Results? to export the results of the script to a variable in the current R workspace (the default variable name is pecboResult).

Explanation of PECBO Output

The inference data frame will have a column with the site identifier, a column for an estimate of environmental conditions computed, and a column labeled "Inconsistent". Sites at which Inconsistent is TRUE are sites in which the solution algorithm did not converge to a single solution. These sites typically do not have enough taxa to confidently infer environmental conditions, so inferences at these sites should be used with caution.