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CADDIS Volume 4: Data Analysis

Predicting Environmental Conditions from Biological Observations (PECBO) Appendix

Topics in Using Existing Taxon-Environment Relationships


This section provides a detailed step-by-step guide for inferring environmental conditions from your local benthic macroinvertebrate data. These inferences use pre-existing taxon-environment relationships for different environmental variables (e.g., stream temperature and bedded fine sediment) that are available in the CADDIS database.

It is assumed in this section that the user has some experience with the command line interface of R and is interested in thoroughly understanding the steps involved in predicting environmental conditions from biological observations. If you have no experience with R, you may want to use the tool for biological inferences provided in CADStat.

A brief review of R command line syntax is provided in the R Primer section.

Computing biological inferences using your local benthic macroinvertebrate data requires four main steps:

  1. Download the library of inference scripts for R and download the appropriate taxon-environment dataset.
  2. Standardize the taxonomy of your biological observations.
  3. Assign operational taxonomic units (OTUs) to your biological observations.
  4. Compute biological inferences for each of your sites.

Using Existing Taxon-Environment Relationships:   Next

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