iNEXTPD2-package: Interpolation and Extrapolation with Phylogenetic Diversity
In YanHanChen/iNEXTPD2: Interpolation and Extrapolation with Phylogenetic Diversity

Description Details Author(s) References

Provides functions for phylogenetic diversity analysis. (1) The 'iNEXT' standardization for phylogenetic diversity: computes and plots rarefaction and extrapolation of phylogenetic diversity based on two types of standardization methods (sample size and sample coverage). (2) The phylogenetic diversity estimation: computes and plots asymptotic phylogenetic diversity profile as a function of diversity order (q-profile) or time (time-profile).

The four main functions are: (1) iNEXTPD computes the 'iNEXT' standardization for phylogenetic diversity via rarefaction and extrapolation. (2) estimatePD computes phylogenetic diversity at specified values of sample coverages. (3) PhdAsy computes asymptotic phylogenetic diversity profiles. (4) PhdObs computes empirical or observed phylogenetic profiles.

Anne Chao, Yan-Han Chen and Chun-Huo Chiu

Maintainer: Anne Chao <chao@stat.nthu.edu.tw>

Chao, A., Chiu C.-H. and Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B., 365, 3599-3609.

Chao, A., Chiu, C.-H., Hsieh, T. C., Davis, T., Nipperess, D., and Faith, D. (2015). Rarefaction and extrapolation of phylogenetic diversity. Methods in Ecology and Evolution, 6, 380-388.

Chao, A., Chiu C.-H. and Jost L. (2016). Phylogenetic diversity measures and their decomposition: a framework based on Hill numbers. pp. 141-172 in Pellens R. and Grandcolas P. (eds) Biodiversity Conservation and Phylogenetic Systematics: Preserving our Evolutionary Heritage in an Extinction Crisis, Springer.

Hsieh, T. C. and Chao, A. (2017). Rarefaction and extrapolation: making fair comparison of abundance-sensitive phylogenetic diversity among multiple assemblages. Systematic Biology, 66, 100-111.