Simultaneous inference for diversity indices.

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Description

Package simboot provides estimation of simultaneous bootstrap and asymptotic confidence intervals for diversity indices, namely the Shannon and the Simpson index. Several pre-specified multiple-comparison types are available. Further user-defined contrast matrices are applicable. In addition, simboot estimates adjusted as well as unadjusted p–values for two of the three proposed bootstrap methods. Further simboot allows for comparing biological diversities of two or more groups with simultaneously testing a user-defined selection of Hill numbers of orders q, which are considered appropriate and useful indices for measuring diversity.

Details

Package: simboot
Type: Package
Version: 0.2-5
Date: 2014-04-10
License: GPL (>= 2)
LazyLoad: yes

Author(s)

Ralph Scherer\ Philip Pallmann\ Maintainer: Ralph Scherer <shearer.ra76@gmail.com>

References

Scherer, R. and Schaarschmidt, F. (2013) Simultaneous confidence intervals for comparing biodiversity indices estimated from overdispersed count data. Biometrical Journal 55, 246–263.

Evaluation of the methods in sbdiv

Pallmann, P. et al. (2012) Assessing group differences in biodiversity by simultaneously testing a user-defined selection of diversity indices. Molecular ecology resources 12, 1068–??78.

Evaluation of the methods in mcpHill

Westfall, P. H. and Young, S. S. (1993) Resampling-Based Multiple Testing: Examples and Methods for p–Value Adjustment. New York: Wiley.

Corresponding method sbdiv with method WYht

Besag, J., Green, P. J., Higdon, D., Mengersen, K. (1995) Bayesian computation and stochastic systems (with discussion) . Statistical Science, 10, 3–66.

Corresponding method sbdiv with method rpht

Beran, R. (1988) Balanced simultaneous confidence sets. Journal of the American Statistical Association, 83, 679–686.

Corresponding method sbdiv with method tsht

Fritsch, K. S., Hsu, J. C. (1999) Multiple comparison of entropies with application to dinosaur biodiversity. Biometrics, 55, 4, 1300–1305.

Rogers, J. A., Hsu, J. C. (2001) Multiple comparisons of biodiversity. Biometrical Journal, 43, 5, 617–625.

Corresponding method sbdiv with method asht

Jost, L. (2008) G(ST) and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.

Corresponding method mcpHill