EstimateS is a free software application for Windows and Macintosh operating systems that computes a variety of biodiversity statistics, estimators, and indices based on biotic sampling data. Some features require species relative abundance data, others only species presence/absence data. A comprehensive User's Guide is available online at this site.
Major Features of EstimateS 9
Nonparametric rarefaction and extrapolation of species accumulation curves
- Computes expected species accumulation curves for rarefied reference samples (both sample-based rarefaction curves and individual-based rarefaction curves, in the terminology of Gotelli & Colwell 2001, 2011), with 95% unconditional confidence intervals, using the analytical formulas of Colwell et al. (2004) and Colwell et al. (2012).
- Computes expected species accumulation curves for augmented reference samples (both sample-based extrapolation curves and individual-based extrapolation curves), with 95% unconditional confidence intervals, using the analytical formulas of Colwell et al. (2012).
Species richness estimators and diversity indices
- Computes non-parametric, asymptotic species richness estimators for abundance-based data (Chao 1 and ACE) and for incidence-based data (Chao2, ICE, first and second order Jackknives, and Bootstrap).
- For Chao1 and Chao 2, computes log-linear confidence intervals.
- Computes Shannon (both H and e^H) and inverse Simpson (Hill numbers 1 and 2), and Fisher's alpha diversity indices.
- All estimators and indices are computed for rarefied samples or individuals to reduce the bias of comparisons.
Shared species estimation and biotic similarity indices, with estimators
- Computes Chao's estimator of total shared species (including observed and unseen shared species) for sample pairs.
- Computes classic Sørensen and Jaccard similarity indices for sample pairs based on incidence (presence-absence) or abundance data sets
- Computes Chao's abundance-based Sørensen and Jaccard similarity indices, with statisically rigorous estimators and their standard errors, for sample pairs based on abundance or on replicated incidence (presence-absence) data sets.
- Computes Morisita-Horn and Bray-Curtis (= "Sørensen quantitative") similarity indices for sample pairs based on abundance data sets.
Importing data and exporting results
- For input, accepts tab-delimited, plain text files (produced by programs such as Excel, using "Save As Tab-delimited Text"), in either of two matrix formats (species-by-sample or , sample-by-species) or either of two "triplet" formats ([species index, sample index, value]; or [sample index, species index, value]).
- For input, accepts pre-formatted sample-by-species matrices exported by Biota: The Biodiversity Database Manager.
- Exports all results as tab-delimited text files, easily opened in Excel, statistical, or graphing applications.
- As an option, records and exports results from n individual randomizations to a text file, allowing computation of precision, accuracy, and other analyses (Walther and Moore 2005), using Excel or other applications.
Two versions of EstimateS are currently offered.
- EstimateS 9.00 runs under Windows 8 and Mac OS 10.8 and earlier operating systems and has many new features.
- EstimateS 8.20 runs under Windows 7 and MacOS 10.6 and earlier operating systems and maintains the traditional interface and tools that EstimateS has offered since 2005.
Who Uses EstimateS?
Between 1997 and 2012, EstimateS was downloaded by more than 60,000 users in more than 100 countries around the globe. They use EstimateS in conservation biology, biotic inventories, natural area assesssment and monitoring, biogeography, macroecology, microbial ecology, molecular biology, ethnobotany, archaeology and many other fields. You can get an idea of the diversity of uses by scanning the titles of the references that appear below.
Publications That Cite EstimateS
As of July, 2004, a total of 237 publications were known to have cited EstimateS. Since then, hundreds of authors have kindly sent citations or pdfs, but I have not been able to find the time yet to list them. According to Google Scholar, "EstimateS: statistical estimation of species richness" has been cited more than 4100 times as of Febuary, 2013. A project to update the online list is currently underway.
If you have cited EstimateS in a published work and you would be willing to have it included, please contact Robert K. Colwell with details.