References

To see the references in qdiv, use:

import qdiv

qdiv.citations(f='all')

Prints a list of references used in the development of qdiv.

f is the qdiv function. For example, f=’diversity.naive_alpha’ prints the references that were especially relevant for developing the diversity.naive_alpha function. f=’all’ prints all references listed below.

qdiv package:

Naive diversity (diversity.naive_alpha, diversity.naive_beta, diversity.naive_multi_beta):

  • Hill, M. O. (1973). Ecology 54(2): 427-432.

  • Jost, L. (2006). OIKOS 113(2): 363-375.

  • Jost, L. (2007). Ecology 88(10): 2427-2439.

Phylogenetic diversity (diversity.phyl_alpha, diversity.phyl_beta, diversity.phyl_multi_beta):

  • Chao, A., C.-H. Chiu and L. Jost (2010). Philosophical Transactions of the Royal Society B: Biological Sciences 365(1558): 3599-3609.

  • Chiu, C. H., L. Jost and A. Chao (2014). Ecological Monographs 84(1): 21-44.

Functional diversity (diversity.func_alpha, diversity.func_beta, diversity.func_multi_beta):

  • Chiu, C. H. and A. Chao (2014). PLoS One 9(7): e100014.

Evenness (diversity.evenness, diversity.dissimilarity_by_feature, plot.dissimilarity_contributions):

  • Chao, A. and C. Ricotta (2019). Ecology 100(12): e02852.

Raup-Crick null model (model.rcq):

  • Raup, D. M. and R. E. Crick (1979). Journal of Paleontology 53(5): 1213-1227.

  • Chase, J. M., N. J. B. Kraft, K. G. Smith, M. Vellend and B. D. Inouye (2011). Ecosphere 2(2): 24.

  • Stegen, J. C., X. Lin, J. K. Fredrickson, X. Chen, D. W. Kennedy, C. J. Murray, M. L. Rockhold and A. Konopka (2013). ISME Journal 7(11): 2069-2079.

  • Modin, O., R. Liébana, S. Saheb-Alam, B.-M. Wilén, C. Suarez, M. Hermansson and F. Persson (2020). Microbiome 8, 132, DOI: 10.1186/s40168-020-00909-7

Phylogenetic null models (model.nriq, model.ntiq, model.beta_nriq, model.beta_ntiq):

  • Webb, C. O., D. D. Ackerly, M. A. McPeek and M. J. Donoghue (2002). Annual Review of Ecology and Systematics 33(1): 475-505.

  • Fine, P. V. A. and S. W. Kembel (2011). Ecography 34: 552-565.

Mantel test (stats.mantel):

  • Mantel, N. (1967). Cancer Research 27(2): 209-220.

Permanova test (stats.permanova):

  • Anderson, M. (2001). Austral Ecology 26(1): 32-46.