Eco-Tools

Summary
Type of tool	Suite of tools
Function	Calculations in ecology and conservation biology
Online / Desktop	Online
Computer infrastructure	Browser
Development status	Last update March 2006
Time of use	As a post process, after data is with the user
Licence

Eco-Tools is a web-accessible means of performing commonly-needed and useful calculations in ecology and conservation biology.1

 

Description

No special software is required, and all algorithms are open-source and based on standard references.

 

The Eco-Tools

Life Tables – Life Table Calculations

This Eco-Tool uses matrix algebra to calculate a variety of statistics based on a table of survivorship and maternity values by age class.2

 

Population Timeseries – Autocorrelograms and Power Spectra

Analytical population Dynamics. Under development. 3

 

Population Genetics – F-statistics

Calculates the statistical outcome over several generations of the action of evolutionary forces on allelic and genotypic frequencies. The four evolutionary forces act on genetic variation by changing the frequency of alleles in a population, and the distribution of alleles among populations.4

 

Population Viability Analysis (PVA) – Simple Count-Based PVA

This Eco-Tool performs a simple count-based population viability analysis. In short, this is the simplest possible form of PVA, based only on a timeseries of censuses of the population in question. 5

 

Species Diversity – Estimating Species Richness

The Species Richness eco-tool implements a variety of analyses that take as their input a “species by sample” matrix of observed abundances. The analyses include various summary statistics, as well as a number of estimators of true species richness, including Chao 1, Chao 2, ACE, ICE, first-order jackknife, second-order jackknife, and bootstrap. Variances (and hence confidence intervals) for these estimators are calculated based on analytical results (for Chao 1 and Chao 2) or on multiple random resamples with replacement (for everything else). Finally, the eco-tool calculates a sample-based rarefaction curve, with confidence intervals, as well as the individual-based rarefaction curve for comparison. These curves are plotted, and both the figures and the curve data are provided for download.6

 

Ordination – Canonical Methods: RDA and CCA

This Eco-Tool implements two forms of canonical ordination: Redundancy Analysis (RDA) and Canonical Correspondence Analysis (CCA). The main input consists of a matrix where rows represent sites and columns contain either dependent variables (typically observations of species abundances) or candidate predictor variables (measurements of some environmental quality at each site). A second input is the number of predictor variables; this is used to divide the input matrix into its two components. A third input is the number of randomizations used to test the significance of the dependent variables in determining the observations. 7

 

Taxonomic and Phylogenetic Autocorrelation – Moran's I

Moran’s I autocorrelation statistics based on taxonomy. Under development.8

 

These tools have been developed by Gareth Russell, Columbia University, and are hosted by the New Jersey Institute of Technology.9 Eco-Tools is open to input from others.

 

Function

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

 

Why use this tool?

This is a set of numerical tools for ecological analysis that are available, free, to anyone with web access. What makes these tools different from other third-party offerings is that they are programmed in Mathematica (Wolfram Research), which is a high-level coding language, and the code is available for anyone to inspect. The idea is that the tools can be easily peer-reviewed, corrected, and improved over time.10

 

Who will use this tool?

• Data users
  • Expert
  • Interest groups
• Special skills required

 

How will the tool be used?

• Data formats vary depending on the tool in use 11
• Online tools, programmed in Mathematica
• User input 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

• Eco-Tools: http://eco-tools.njit.edu/webMathematica/EcoTools/
• Contact: admin@eco-tools.net
• Cost: free

 

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