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The Pinkham-Pearson Index

Page history last edited by pinkhamc@... 10 years, 10 months ago

The following is divided into two major sections:  History and Use


History of the Pinkham-Pearson Index


The Pinkham-Pearson Index was published in 1976:

Pinkham, C.F.A., and Pearson, J.G.  1976.  Applications of a new coefficient of similarity to pollution surveys. J. Water Pollut. Control Fed., 48, 717. (53). Since this paper no longer appears to be available from the journal, click here for a copy: 76 PaperScan.doc .


It was developed as a result of our need to test the community structure of animal and plant populations on Carroll Island in the upper Chesapeake Bay.  One half of the island had been exposed to limited open-air testing of chemical and biological agents and simulants before President Nixon unilaterally banned the practice on November 25th, 1969. See President Nixon’s Decision to Renounce the U.S. Offensive Biological Weapons Program. The two halves were separated by a wide marsh, thus we had a control portion which had not been exposed and an experimental portion which had.  The newly-formed Ecology Branch (Under the able leadership of Dr. F. Prescott Ward) at the Biomedical Research Center at Edgewood Arsenal was asked to answer the question, "Did the testing have any lingering effect upon the biota of the test site and downwind areas?"   Gareth and I (both commissioned officers with advanced degrees) were responsible for the aquatic and terrestrial investigations, respectively.  We and our colleagues utilized standard techniques to sample aquatic plants, macroinvertebrates, fishes, and reptiles, and terrestrial plants, amphibians, reptiles, birds, and mammals.  Thus we had this huge amount of data from both sites but no reliable way to compare them.  The indexes available at the time were primarily focused on measuring diversity.  We didn't want to measure diversity; we wanted to compare community structure.  So one evening, Gareth and I gathered our data, a huge sheet of paper, a six-pack of beer and tackled the problem on the floor of his apartment.  (He and I lived across the hall from each other in officer's housing in Ryder Court-which is how I got involved in the program in the first place, but that's another story.)  It really didn't take us long to develop the index.  We next had to write the computer program that would apply it to the data.  Fortunately, I had written a similar program in Fortran 4 for my doctoral thesis, so that part was fairly easy as well.


In short, this index, which has now become one of the more powerful tools for comparing community structure, came about through a convergence of unlikely circumstances.  But then, isn't that how most of science advances?


In anticipation of your logical question, we never found any evidence that the testing had a residual effect upon the community structure of the animals and plants of Carroll Island.  Both communities were robust.


Use of the Pinkham-Pearson Index


BioSim2 Program (Latest Version)


   With Windows XP at least, when downloading the biosim2-0-03h.jar file, Windows tries to save it as
      biosim2-0-03.zip. If this happens to you, save it as ".jar" or rename it after saving it as ".jar".
   Please send us your suggestions for improvement.


User's Manual (EPA Publication-pdf file)



Relevant Publication (email pinkhamc@norwich.edu for copy)

Pearson, J.G., and C.F.A. Pinkham.  1992.  Strategy for data analysis in environmental surveys emphasizing the index of biotic similarity and BIOSIM1. Water Environ. Res., 64:901-909. (52)  This article also appears to be no longer available from the journal, so click here for a copy: 92 PaperScan.doc  


Recent Examples of Application of BioSim2

·              3/17/05,  J. Gareth Pearson, Brian P. Reid and Victor T. Chevalier, Demonstration of the Java version of the Pinkham-Pearson index for the comparison of community structure, 29th Annual Meeting of the New England  Association of Environmental Biologists – EPA, Lake George, NY (Poster Presentation)
NEAEB POSTER.ppt  (Power Point Version)    NEAEB poster.doc  (MS Word Version)

·              6/08/05, Fiske, Steven, & C.F.A. Pinkham, Use of BioSim2 to identify relationships between biotic and abiotic parameters for small, moderate gradient, Vermont streams, 11th Annual Meeting of the North Atlantic Branch of the Society of Environmental Toxicology and Chemistry, Burlington, VT (Platform Presentation)
·              3/30/06, Pinkham, C. F.A., BioSim2, 30th Annual Meeting of the New England  Association of Environmental Biologists , Bethel, ME  (Workshop)
BioSim2WS.ppt  (Power Point Presentation with Notes-5 MB file)

·              3/14/07, Olsen, Darlene and C. F. A. Pinkham, Using BioSim2 to identify statistically-valid sectors of indicator taxa, 31stAnnual Meeting of the New England  Association of Environmental Biologists , Mount Snow, VT (Platform Presentation)
PresentationNEAEB07.ppt  (Power Point Presentation with Notes-6 MB file)

·              6/6/07, Olsen, Darlene,  C. F. A. Pinkham, J. G. Pearson, and B.P. Reid, The use of the Pinkham-Pearson Index for the comparison of community structure in BioSim2 to identify statistically-valid sectors of indicator taxa with sites, 55th Annual Meeting of the North American Benthological Society, Columbia, NC (Platform Presentation)
332_Pinkham.ppt  (Power Point Presentation with Notes-4 MB file)

·              6/4/08, C. F. A. Pinkham, Olsen, Darlene, J. G. Pearson, and B.P. Reid, The use of the Pinkham-Pearson Index for the comparison of community structure in BioSim2 to identify statistically-valid sectors of taxa, Streams Project Training Session, UVM (Platform Presentation)  This presentation includes the story of how and why  the Index was developed.

PresentationStreamsProject08.ppt  (Power Point Presentation with Notes-5 MB file)

           3/19/10, Pinkham, C. F. A., Declan J. McCabe, Farley Brown, and Johnathon L. Miller, Application of the Index of Biotic Similarity (B) to the Analysis of the Data Generated by the Vermont EPSCoR Streams Project.  34th Annual Meeting of the New England  Association of Environmental Biologists , Newport, RI, (Platform Presentation)  

Steams Project_NEAEB10.pptx (Power Point Presentation with Notes-5 MB file)



Programs designed to facilitate your data analysis using the row and column dendrograms and the original data matrix rearranged in double-dendrogram order produced by BioSim2.  (Feel free to contact Carl Pinkham with any question.)


1) Moving from the original data matrix rearranged in double dendrogram order produced by BioSim2 2_CPCRW_Reordered_Data.xls (Excel file) to a matrix with sectors delineated by lines using both the row dendrogram and the column dendrograms:



and the row cophenetic correlation coefficient and the column cophenetic correlation coefficient



Use the following sheets and the above plots to see how sectors are set up:

3a_Determining_Sectors_Sheets.xls  (Excel file)


2)  Scaling the original data matrix using Excel, with instructions and a sample data set

1_Scaling Sheet_2.xls  (Excel file)
(Scaling is used when the original data set exists with different units as, e.g., would happen if you are comparing density values with physical parameters such as pH and temperature.)


     Statistical analysis of sectors, with an example with instructions and the run program (Excel file)

     Semiquantitative analysis of sectors using Excel, with instructions
          Step 1 Summarizing sector values (Excel file)
          Step 2 Coding all sectors for presentation/publication (Excel file)


If you wish to be notified of updates as soon as they happen, send email to: pinkhamc@norwich.edu
(As a minimum, please provide your name, title, address and work phone.)


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