User's Manual for the National Water-Quality Assessment Program Invertebrate Data Analysis System (IDAS) Software: Version 3 OFR 03-172 By Thomas F. Cuffney

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Abstract

The Invertebrate Data Analysis System (IDAS) software provides an accurate, consistent, and efficient mechanism for analyzing invertebrate data collected as part of the National Water-Quality Assessment Program and stored in the Biological Transactional Database (Bio-TDB). The IDAS software is a stand-alone program for personal computers that run Microsoft (MS) Windows®. It allows users to read data downloaded from Bio-TDB and stored either as MS Excel® or MS Access® files. The program consists of five modules. The Edit Data module allows the user to subset, combine, delete, and summarize community data. The Data Preparation module allows the user to select the type(s) of sample(s) to process, calculate densities, delete taxa based on laboratory processing notes, combine lifestages or keep them separate, select a lowest taxonomic level for analysis, delete rare taxa, and resolve taxonomic ambiguities. The Calculate Community Metrics module allows the user to calculate over 130 community metrics, including metrics based on organism tolerances and functional feeding groups. The Calculate Diversities and Similarities module allows the user to calculate nine diversity and eight similarity indices. The Data export module allows the user to export data to other software packages and produce tables of community data that can be imported into spreadsheet and word-processing programs. Though the IDAS program was developed to process invertebrate data downloaded from USGS databases, it will work with other data sets that are converted to the USGS (Bio-TDB) format. Consequently, the data manipulation, analysis, and export procedures provided by the IDAS program can be used by anyone involved in using benthic macroinvertebrates in applied or basic research.

Table of Contents

• Abstract
• Introduction
  • Purpose and scope
  • Acknowledgments
• Invertebrate Data Analysis System (IDAS)
  • Capabilities
  • Sources of data used by IDAS
  • Characteristics of Bio-TDB data
    • Provisional and conditional identifications
    • Ambiguous taxa
  • Installation
    • System requirements
    • Installing the IDAS software
    • Updates
  • Help and documentation
• Using IDAS
  • Starting IDAS
  • Common features of modules
    • Menu items
    • Status bars
    • Loading data
    • Resetting or exiting a module
• Edit Data module
  • Subset data
    • Sample information
    • Taxonomy
  • Combine/delete data
  • Summarize taxa
• Data Preparation module
  • Processing options
    • Select sample type(s) to process
    • Calculate densities
    • Data deletions based on NWQL BG processing notes
    • Data deletions based on lifestages
    • Options based on combining lifestages
    • Options for forming qualitative (QUAL) samples
    • Select lowest taxonomic level
    • Delete rare taxa
    • Options for resolving ambiguities
      • Sample-by-sample basis
        • Option 1 (RS1): Delete ambiguous parents and retain children
        • Option 2 (RS2): Delete children of ambiguous parents and add their abundances to the abundance of the ambiguous parent
        • Option 3 (RS3): If the abundance of an ambiguous parent is greater than the sum of the abundances of the children, add the children's abundances to that of the parent and delete the children; otherwise, retain the children and delete the parent
        • Option 4 (RS4): Distribute ambiguous parent abundance among children in accordance with the relative abundance of each child
        • Option 5 (RS5): None—retain ambiguous taxa
      • Combined samples
        • Option 1 (RC1): Delete ambiguous parents and retain children
        • Option 2 (RC2): Delete children of ambiguous parents and add their abundances to the abundance of the ambiguous parent
        • Option 3 (RC3): If an ambiguous parent's abundance is greater than the sum of the children's abundances, add the children's abundances to the parent and delete the children. Otherwise, retain the children and delete the parent
        • Option 4 (RC4): Distribute ambiguous parent abundance among children in accordance with the relative abundance of each child
        • Option 5 (RC5): None—retain ambiguous taxa
        • Associating ambiguous children with ambiguous parents
  • Running the Data Preparation module
  • Output from the Data Preparation module
  • Resetting or exiting the module
• Calculate Community Metrics module
  • Processing options
  • Updating attributes file
  • Output from the module
  • Resetting or exiting the module
• Calculate Diversities and Similarities module
  • Processing options
  • Output from the module
  • Resetting or exiting the module
• Data Export module
  • Processing options
  • Duplicate sort codes
  • Resetting or exiting the module
• Troubleshooting
  • Types of errors
  • Error messages
  • Reporting program bugs
  • Abnormal termination of IDAS
• Summary
• References cited
• Appendix I: Bio-TDB data file formats
• Appendix II: Data output formats produced by the Data Preparation module
• Appendix III: Data output formats produced by the Calculate Community Metrics module
• Appendix IV: Data output formats produced by the Calculate Diversities and Similarities module
• Appendix V: Data output formats produced by the Data Export module
• Appendix VI: Error messages

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