Biodiversity Statistics and Analysis

This site describes a number of freely available statistics and analysis packages relevant to diversity data.

Description

Software that is listed here is available freely on the Internet, or was developed by Roeland Kindt during the preparation of his PhD thesis. The aim of the thesis was to explore methods of analysing biodiversity data using the management by farmers of tree species diversity in Kenya.1

The software listed here is a collection of free software available for the analysis of diversity data.2

• PopTools - an Excel add-in that allows more complicated analyses to be conducted within Excel.
• EstimateS - provides species accumulation curves, and various estimators of total diversity (gamma diversity).
• PAST - includes many of the functions which are commonly use in palaeontology and palaeoecology. Many of these functions are common to biodiversity analysis as well.
• EcoSim - an interactive program for null model analysis in community ecology.
• Biodiversity Professional - supports the calculation of various diversity indices, clustering and ordination.
• Krebswin - based on the textbook Ecological Methodology by Charles Krebs.
• Multiple linear regression - computes a multiple linear regression and performs tests of significance of the equation parameters using permutations.
• K-Means - a least-squares partitioning method allowing users to divide a collection of objects into K groups.
• DistPCoA - performs Principal Coordinate Analysis with the option of correcting for negative eigenvalues.
• Polynomial RdaCca - performs two forms of canonical analysis, linear and polynomial redundancy analysis and canonical correspondence analysis.
• R - a general statistics package, supporting an environment similar to the S-Plus Package.
• Vegan - conducts many types of ecological and community analysis.
• mgcv - conducts GAM – Generalised Additive Models.
• Instat - a general statistics Package.
• Reading SSC Add-Ins - an Excel add-in that is targeted to more general Types of Analysis.
• ExactS - calculates the exact average species richness for random accumulation of sites.
• ExactSN - calculates the exact average species richness for random accumulation of individuals using the formula for rarefaction.
• SpeciesRichRef - calculates the average species richness for a fixed number of randomly accumulated sites.
• SpeciesRichClus - calculates the average species richness for sites that are randomly clustered in a fixed number of clusters of fixed size.
• DiversityRef - calculates the averages for various diversity indices for a fixed number of randomly accumulated sites.
• RenyiAccum - calculates average accumulation patterns for the Rényi diversity series.
• RenyiRefs - calculate the average values for selected scales of the Rényi diversity and evenness profiles.
• Metapopulation - calculates the average allelic diversity that remains in an age-structured dioecious metapopulation.

Function

• Data manipulation
• Analysis tools
• User interface
  • Personal use
  • Raw data and visual presentation

Why use this tool?

Resources and guidelines useful for statistical analysis of diversity data:3

• Averages
• Regression and analysis of variance
• Species richness
• Diversity indices
• Ecological distance
• Clustering
• Ordination

 Who will use this tool?

• Data users
  • Expert
  • Interest groups
• Statistics skills are required

 How will the tool be used?

• Desktop applications
• Some programs stand alone, others are Excel add-ins and supplements to other applications.
• User input is required

 Where in the data chain could this tool be used?

• User’s machine

 When could this tool be used?

• As a post process, after data is with the user

Availability

• ICRAF - World Agroforestry Centre: http://www.worldagroforestry.org/newwebsite/sites/rsu/index.asp
• Biodiversity Analysis: http://www.worldagroforestry.org/newwebsite/sites/rsu/resources/biodiversity/index.asp
• Software: http://www.worldagroforestry.org/newwebsite/sites/rsu/resources/biodiversity/software/index.asp
• Roeland Kindt Thesis: http://www.worldagroforestry.org/newwebsite/sites/rsu/resources/biodiversity/Thesis/ThesisComplete.pdf
• Cost: free
• Copyright. Varies, see individual programs.
• No warranty

Comments

Many of these applications are becoming dated. Listed dates are up to 2002, though many have been upgraded since.