Related Links

  • Anne Chao's SPADE (Species Prediction And Diversity Estimation) and iNEXT (iNterpolation and EXTrapolation).

SPADE and the SPADE User's Guide can be downloaded at the SPADE website.

iNEXT can be used online here. iNEXT computes some of the same statistics as EstimateS, plus others (especially coverage-based rarefaction and extrapolation) that EstimateS does not compute.

For iNext, the user provides a vector of abundances of individual species (abundance data) or incidences of individual species (incidence data). iNEXT computes the following species richness estimates and associated 95% confidence intervals:

  • Sample-size-based rarefaction and extrapolation: species richness estimates for rarefied and extrapolated samples up to a size specified by the user (i.e., an endpoint, see below). Refer to Colwell et al. (2012) for details.
  • Coverage-based rarefaction and extrapolation: species richness estimates for rarefied and extrapolated samples for sample coverage up to a coverage specified by the user (i.e., an endpoint, see below). Refer to Chao and Jost (2012) for details.

iNEXT also plots the following three integrated sampling curves suggested in Chao et al. (2013) for unified sampling and estimation in species diversity analysis.

  • Sample-size-based rarefaction and extrapolation sampling curve: this curve plots the species richness estimates for a rarefied and extrapolated sample with respect to sample size up to a specified endpoint.
  • Sample completeness curve: this curve plots the sample completeness (as measured by sample coverage) with respect to sample size. The curve provides a bridge between sample-size- and coverage-based rarefaction and extrapolation.
  • Coverage-based rarefaction and extrapolation sampling curve: this curve plots the species richness estimates for rarefied sample and extrapolated sample with respect to sample coverage up to a specified endpoint.
  • SAM: Spatial Analysis in Macroecology. SAM, downloadable freeware developed by Thiago Rangel and colleagues, is a compact but robust computer program designed as a package of statistical tools for spatial analysis, mainly for applications in Macroecology and Biogeography. SAM runs under Microsoft Windows as as a user-friendly, menu-driven, graphical interface computational program. SAM offers a wide spectrum of statistical methods currently used in Surface Pattern Spatial Analysis. Sam fills most current scientific and analytical needs of Macroecologists, Biogeographers and Geographical Ecologists who study broad scale biological patterns and processes.

  • BioDiversity Pro. BioDiversity Pro was designed and developed by Neil McAleece. This package was devised jointly by P.J.D. Lambshead and G.L.J. Paterson of the The Natural History Museum in London and J.D. Gage of the Scottish Association for Marine Science, Oban, Scotland.
  • Jari Oksanen's VEGAN Package for R. The VEGAN package is intended to help vegetation ecologists and other community ecologists to use R. It contains all major ordination methods, ecologically meaningful dissimilarity indices, tools to analysis of diversity, species richness and abundance models, plus numerous support functions
  • If you would like to see a link to your software here, please write.

©2013
Robert K. Colwell