Instructions for using the RIVPACS Benthic Index Calculator Tool

This tool was developed to provide an easy way for people to upload their benthic data and have the RIVPACS Benthic Index calculated for each of their sites. The tool uses an Excel based template to submit data for analysis. The calculations are made using script in the R programing language.

The RIVPACS index calculates the number of reference taxa present in the test sample (observed or "O") and compares it to the number expected to be present ("E") in a reference sample from the same habitat.

Here are the steps necessary to successfully upload your data:

  1. Download the RIVPACS excel template from the RIVPACS Calculator Tool website.
  2. Fill in columns A through E on the StationInfo tab. This includes StationID, Sample Depth (must be in meters), Latitude (decimal degrees), Longitude (decimal degrees and must be negative) and the HabitatCode ("C" for southern California Marine Bays and Estuaries and "D" for San Francisco Polyhaline).
  3. Fill in columns A through C on the Benthic tab with StationID, taxa, and abundance. If multiple stations are entered, the lines of data need not be contiguous for each station nor in the same station order as the StationInfo tab. It is IMPORTANT not to move (cut and paste) lines of data once they have been entered into the sheets. Names of the tabs within the input file must not be changed.
  4. Check your data using Column D. When you fill in Column B a check is done against the Southern California Association of Marine Invertebrate Taxonomists (SCAMIT) Edition 5 list (TaxaList tab in the Excel workbook).
    1. Column D is used to check your species against the SCAMIT List. If your taxa name matches a taxa on this list you will see the word "Correct" in column D. If you see the word "Wrong" in Column D, your taxa does not match any on the SCAMIT list. This may be due to a misspelling in your data or a difference in taxonomic nomenclature or identification. Spelling is critical, including punctuation (e.g. no periods after "sp"), capitalization, and abbreviations. The TaxaList page can be consulted for help with proper spelling.
    2. Column D has formulas for the checks down to row 30000. If you have data that goes beyond row 30000 please copy and paste the formula down to the end of your data. We do this to limit the size of the template for downloading.
  5. Once you have filled in the template, you are ready to submit your data. From the RIVPACS Calculator Tool Website you can click on the Browse button, choose your file, and click on Open. In addition, you can also drag and drop your file in the box on the web page (Note: this feature does not work if you are using Internet Explorer). Your file will be automatically processed. The progress can be followed on the right-hand side of the page. If the tool detects certain types of errors (e.g. invalid habitat codes) a message will pop up explaining the error(s) and detailing where they occur in your file. Any errors need to be corrected and the file resubmitted.
  6. Once your file is successfully submitted, the results will appear automatically in a series of links on the page, organized by habitat (southern California and San Francisco Bay). You can click on the links to see specific RIVPACS output. The output pages are in HTML format which can be saved. The saved HTML files can then be opened in Excel or Word for data manipulation and use in other index or assessment tools.
    1. The RIVPACS Output page has O/E data that is the key result. This page contains the calculated number of observed reference species ("O"), expected species ("E"), and then the ratio ("O/E"). This page also shows the results of outlier checking which determines whether the stations belong in their designated habitat based on taxa, latitude, longitude and depth.
    2. The Probability Comparison link contains the reference taxa predicted but not observed and the taxa not predicted but observed in separate tables. For each taxa, the stations at which it was found or not found (depending on which table you are viewing) are shown along with the probability of that taxon being found at those stations. There is also a table indicating the taxa which were predicted and also observed.
    3. The Probability Matrix shows the predicted occurrence probability for each of the reference taxa used in the RIVPACS calculation.
  7. You can submit multiple files for calculation and a new set of links will appear for each submittal. A history button in the upper right-hand corner contains all of the results from all files submitted in a session.