Species Richness v2.1

Introduction

The Species Richness eco-tool implements a variety of analyses that take as their input a “species by sample” matrix of observed abundances. For the most part, these are a subset of the analyses performed by the downloadable software package EstimateS (Colwell 1994–present). 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 (see Colwell and Coddington 1994 for an overview of these estimators). 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, using the analytical method described in Colwell et al. 2004, 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.

Differences between the eco-tool and EstimateS

What the Eco-Tool does (that EstimateS does not)

What the Eco-Tool does NOT do (that EstimateS does)

Why duplicate EstimateS, even in part? Does Rob Colwell know about this?

Good questions! The eco-tool provides access to many of the same calculations for those who, for one reason or another, cannot use the latest versions of EstimateS. This may include those with access only to very old computers, or those using UNIX. The eco-tool provides plots for instant visual feedback, and the web-page nature of the output means that explanatory text can accompany the statistics. It is also easier (therefore quicker) to fix bugs and implement updates in the higher-level code that runs the eco-tool. The source code is available for download in a fully-annotated Mathematica notebook, with example data built in, so it can be verified and/or customized. Finally, it is always good to have an alternative source of calculations to compare against, as this is how mistakes are found!

And yes, Rob knows and approves.

References

Colwell, R. K and J. A. Coddington (1994) Estimating terrestrial biodiversity through extrapolation. Phil. Trans Roy. Soc. Lond. B 345: 101–118.

Colwell, R. K. 1994–present. EstimateS: statistical estimation of species richness and shared species from samples. http://viceroy.eeb.uconn.edu/estimates. [Persistent URL: http://purl.oclc.org/estimates.]

Colwell, R. K., C. X. Mao and J. Chang (2004) Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85: 2717–2727.

Gotelli, N. and R. K. Colwell (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters 4: 379–391.

Chao, A., Chazdon, R. L., Colwell, R. K. and Shen, T.-J.(2005). A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecology Letters 8: 148–159.

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