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hilldiv: an R package for the integral analysis of diversity based on Hill numbers

View ORCID ProfileAntton Alberdi, View ORCID ProfileM Thomas P Gilbert
doi: https://doi.org/10.1101/545665
Antton Alberdi
1Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1350 Copenhagen, Denmark.
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M Thomas P Gilbert
1Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, 1350 Copenhagen, Denmark.
2NTNU University Museum, N-7491 Trondheim, Norway.
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Abstract

  1. Hill numbers provide a powerful framework for measuring, estimating, comparing and partitioning the diversity of biological systems as characterised using high throughput DNA sequencing approaches. However, the implementation of Hill numbers in this context remains limited.

  2. In order to facilitate the implementation of Hill numbers into such analyses, whether focussing on diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses, we present a new R package. ‘Hilldiv’ provides a set of functions to assist analysis of diversity based on Hill numbers, using OTU tables and associated phylogenetic trees as inputs.

  3. Multiple functionalities of the library are introduced, including (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these are grounded in abundance-based and incidence-based Hill numbers.

  4. We provide a supplement that demonstrates the package’s main functions using an OTU table representing the diet of eight bat species. The package can be directly installed from github (https://github.com/anttonalberdi/hilldiv).

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 10, 2019.
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hilldiv: an R package for the integral analysis of diversity based on Hill numbers
Antton Alberdi, M Thomas P Gilbert
bioRxiv 545665; doi: https://doi.org/10.1101/545665
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hilldiv: an R package for the integral analysis of diversity based on Hill numbers
Antton Alberdi, M Thomas P Gilbert
bioRxiv 545665; doi: https://doi.org/10.1101/545665

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