simboot-package: Simultaneous inference for diversity indices.
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
ll{
Package: simboot
Type: Package
Version: 0.2-0
Date: 2013-02-20
License: GPL-2
LazyLoad: yes
}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