citations.bib

@article{halko2011,
	title = {An Algorithm for the Principal Component Analysis of Large Data Sets},
	copyright = {Copyright © 2011 Society for Industrial and Applied Mathematics},
	url = {https://epubs.siam.org/doi/abs/10.1137/100804139},
	doi = {10.1137/100804139},
	abstract = {Recently popularized randomized methods for principal component analysis (PCA) efficiently and reliably produce nearly optimal accuracy—even on parallel processors—unlike the classical (deterministic) alternatives. We adapt one of these randomized methods for use with data sets that are too large to be stored in random-access memory (RAM). (The traditional terminology is that our procedure works efficiently out-of-core.) We illustrate the performance of the algorithm via several numerical examples. For example, we report on the PCA of a data set stored on disk that is so large that less than a hundredth of it can fit in our computer's RAM.},
	language = {en},
	urldate = {2022-02-22},
	journal = {SIAM Journal on Scientific Computing},
	author = {Halko, Nathan and Martinsson, Per-Gunnar and Shkolnisky, Yoel and Tygert, Mark},
	month = {oct},
	year = {2011},
	note = {Publisher: Society for Industrial and Applied Mathematics},
}

@article{mcdonald2018unifrac,
  title={Striped UniFrac: enabling microbiome analysis at unprecedented scale},
  author={McDonald, Daniel and Vázquez-Baeza, Yoshiki and Koslicki, David and McClelland, Jason and Reeve, Nicolai and Xu, Zhenjiang and Gonzalez, Antonio and Knight, Rob},
  journal={Nature Methods},
  year={2018},
  publisher={Nature Publishing Group},
  doi={10.1038/s41592-018-0187-8}
}

@article{lozupone2005unifrac,
  title={UniFrac: a new phylogenetic method for comparing microbial communities},
  author={Lozupone, Catherine and Knight, Rob},
  journal={Applied and environmental microbiology},
  volume={71},
  number={12},
  pages={8228--8235},
  year={2005},
  publisher={Am Soc Microbiol},
  doi={10.1128/AEM.71.12.8228-8235.2005}
}

@article{lozupone2007quantitative,
  title={Quantitative and qualitative $\beta$ diversity measures lead to different insights into factors that structure microbial communities},
  author={Lozupone, Catherine A and Hamady, Micah and Kelley, Scott T and Knight, Rob},
  journal={Applied and environmental microbiology},
  volume={73},
  number={5},
  pages={1576--1585},
  year={2007},
  publisher={Am Soc Microbiol},
  doi={10.1128/AEM.01996-06}
}

@article{chang2011variance,
  title={Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny},
  author={Chang, Qin and Luan, Yihui and Sun, Fengzhu},
  journal={BMC bioinformatics},
  volume={12},
  number={1},
  pages={118},
  year={2011},
  publisher={BioMed Central},
  doi={https://doi.org/10.1186/1471-2105-12-118}
}

@article{chen2012associating,
  title={Associating microbiome composition with environmental covariates using generalized UniFrac distances},
  author={Chen, Jun and Bittinger, Kyle and Charlson, Emily S and Hoffmann, Christian and Lewis, James and Wu, Gary D and Collman, Ronald G and Bushman, Frederic D and Li, Hongzhe},
  journal={Bioinformatics},
  volume={28},
  number={16},
  pages={2106--2113},
  year={2012},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/bts342}
}

@article{faith1992conservation,
  title={Conservation evaluation and phylogenetic diversity},
  author={Faith, Daniel P},
  journal={Biological conservation},
  volume={61},
  number={1},
  pages={1--10},
  year={1992},
  publisher={Elsevier},
  doi={https://doi.org/10.1016/0006-3207(92)91201-3}
}

@article{vazquez2013emperor,
  title={EMPeror: a tool for visualizing high-throughput microbial community data},
  author={V{\'a}zquez-Baeza, Yoshiki and Pirrung, Meg and Gonzalez, Antonio and Knight, Rob},
  journal={Gigascience},
  volume={2},
  number={1},
  pages={16},
  year={2013},
  publisher={BioMed Central},
  doi={10.1186/2047-217X-2-16}
}

@article{sorensen1948method,
  title={A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
  author={S{\o}rensen, Thorvald},
  journal={Biol. Skr.},
  volume={5},
  pages={1--34},
  year={1948}
}

@article{jaccard1908nouvelles,
  title={Nouvelles recherches sur la distribution floral},
  author={Jaccard, P},
  journal={Bull. Soc. Vard. Sci. Nat},
  volume={44},
  pages={223--270},
  year={1908}
}

@article{pielou1966measurement,
  title={The measurement of diversity in different types of biological collections},
  author={Pielou, Evelyn C},
  journal={Journal of theoretical biology},
  volume={13},
  pages={131--144},
  year={1966},
  publisher={Elsevier},
  doi={https://doi.org/10.1016/0022-5193(66)90013-0}
}

@article{clarke1993method,
  title={A method of linking multivariate community structure to environmental variables},
  author={Clarke, KR and Ainsworth, M},
  journal={Marine ecology progress series},
  pages={205--219},
  year={1993},
  publisher={JSTOR},
  doi={https://doi.org/10.3354/meps092205}
}

@article{kruskal1952use,
  title={Use of ranks in one-criterion variance analysis},
  author={Kruskal, William H and Wallis, W Allen},
  journal={Journal of the American statistical Association},
  volume={47},
  number={260},
  pages={583--621},
  year={1952},
  publisher={Taylor \& Francis},
  doi = {10.1080/01621459.1952.10483441},
}

@article{anderson2001new,
  title={A new method for non-parametric multivariate analysis of variance},
  author={Anderson, Marti J},
  journal={Austral ecology},
  volume={26},
  number={1},
  pages={32--46},
  year={2001},
  publisher={Wiley Online Library},
  doi={https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x}
}

@article{mantel1967detection,
  title={The detection of disease clustering and a generalized regression approach},
  author={Mantel, Nathan},
  journal={Cancer research},
  volume={27},
  number={2 Part 1},
  pages={209--220},
  year={1967},
  publisher={AACR}
}

@article{pearson1895note,
  title={Note on regression and inheritance in the case of two parents},
  author={Pearson, Karl},
  journal={Proceedings of the Royal Society of London},
  volume={58},
  pages={240--242},
  year={1895},
  publisher={JSTOR},
  doi={https://doi.org/10.1098/rspl.1895.0041}
}

@article{spearman1904proof,
  title={The proof and measurement of association between two things},
  author={Spearman, Charles},
  journal={The American journal of psychology},
  volume={15},
  number={1},
  pages={72--101},
  year={1904},
  publisher={JSTOR},
  doi={https://doi.org/10.2307/1422689}
}

@inbook{legendrelegendre,
  author    = {Pierre Legendre and Louis Legendre},
  title     = {Numerical Ecology},
  publisher = {Elsevier},
  year      = {2012},
  isbn      = {0444-89249},
  edition   = {Third},
  pages     = {499}
}

@Article{Faith1987,
  author={Faith, Daniel P. and Minchin, Peter R. and Belbin, Lee},
  title={Compositional dissimilarity as a robust measure of ecological distance},
  journal={Vegetatio},
  year={1987},
  volume={69},
  number={1},
  pages={57--68},
  abstract={The robustness of quantitative measures of compositional dissimilarity between sites was evaluated using extensive computer simulations of species' abundance patterns over one and two dimensional configurations of sample sites in ecological space. Robustness was equated with the strength over a range of models, of the linear and monotonic (rank-order) relationship between the compositional dissimilarities and the corresponding Euclidean distances between sites measured in the ecological space. The range of models reflected different assumptions about species' response curve shape, sampling pattern of sites, noise level of the data, species' interactions, trends in total site abundance, and beta diversity of gradients.},
  doi="10.1007/BF00038687",
}

@Manual{Oksanen2018,
  title = {vegan: Community Ecology Package},
  author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
  year = {2018},
  note = {R package version 2.5-3},
  url = {https://CRAN.R-project.org/package=vegan},
}