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.