Analysis of community ecology data in R

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====== References ======
<wrap lo>This is a list of references for papers and books used or referred to within this website. Some references contain DOI and, if available in the public domain, also the link to the pdf or HTML version.</wrap>

  * Anderson, M.J., Crist, T.O., Chase, J.M., Vellend, M., Inouye, B.D., Freestone, A.L., Sanders, N.J., Cornell, H.V., Comita, L.S., Davies, K.F., Harrison, S.P., Kraft, N.J.B., Stegen, J.C. & Swenson, N.G. 2011. Navigating the multiple meanings of β diversity: a roadmap for the practising ecologist. //Ecology Letters// 14: 19-28. https://doi.org/10.1111/j.1461-0248.2010.01585.x [[https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1461-0248.2010.01552.x|pdf]]
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  * Borcard, D., Gillet, F. & Legendre, P. 2018. //Numerical Ecology with R. Second edition//. Springer. [[http://adn.biol.umontreal.ca/~numericalecology/numecolR/|Supplementary material]]
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  * Chao, A., Chiu, C.-H. & Jost, L. 2014. Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers. //Annual Review of Ecology, Evolution, and Systematics// 45:297–324.
  * Chao, A., Gotelli, N.J., Hsieh, T.C., Sander, E.L., Ma, K.H., Colwell, R.K. & Ellison, A.M. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. //Ecological Monographs// 84: 45–67. 
  * Dray, S., Choler, P., Dolédec, S., Peres-Neto, P., Thuiller, W., Pavoine, S., ter Braak, C.J.F. (2014): Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation. //Ecology// 95:14-21. https://doi.org/10.1890/13-0196.1
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  * Jurasinsky, G., Retzer, V., Beierkuhnlein, C. 2009. Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity. //Oecologia// 159:15–26.
  * Kent, M. 2011. //Vegetation Description and Data Analysis: A Practical Approach, 2nd Edition//.  Wiley-Blackwell, 428 pp.
  * Legendre, P. & Legendre, L. 1998. //Numerical Ecology//. Second English edition. Developments in Environmental Modelling 20, Elsevier.
  * Legendre, P. & Legendre, L. 2012. //Numerical Ecology//. Third English edition. Elsevier Science BV, Amsterdam.
  * Legendre, P. & Gallagher, E.D. 2001. Ecologically meaningful transformation for ordination of species data. //Oecologia//, 129: 271-280. [[http://adn.biol.umontreal.ca/~numericalecology/Reprints/Legendre_&_Gallagher.pdf|pdf]]
  * Legendre, P. & De Cáceres, M. 2013. Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. 16: 951-963. [[http://adn.biol.umontreal.ca/~numericalecology/Reprints/Legendre_De_Caceres_ELE_2013_app.pdf|pdf]]
  * Lepš, J. & Šmilauer, P. 2003. //Multivariate Analysis of Ecological Data using CANOCO//. Cambridge Press. [[http://regent.jcu.cz/maed/|Supplementary materials]]
  * McCune, B. 1994. Improving community analysis with the Beals smoothing function. //Ecoscience// 1: 82-86.
  * McCune, B. 1997. Influence of noisy environmental data on canonical correspondence analysis. //Ecology// 78: 2617-2623. [[http://people.oregonstate.edu/~mccuneb/McCune1997Ecology78NoisyEnvironmentalCCA.pdf|pdf]]
  * McCune, B. & Keon, D. 2002. Equations for potential annual direct incident radiation and heat load. //Journal of Vegetation Science// 13: 603-606. [[http://people.oregonstate.edu/~mccuneb/JVSreprint13.603-606.pdf|pdf]]
  * McCune, B. & Grace, J.B. 2002. //Analysis of Ecological Communities//. MjM Software, Gleneden Beach, Oregon, USA.
  * Mueller-Dombois, D. & Ellenberg, H. 1974. //Aims and Methods of Vegetation Ecology//. John Wiley & Sons.
  * Murtagh, F. & Legendre, P. 2014. Ward’s hierarchical agglomerative clustering method: which algorithms implement ward’s criterion? //Journal of Classification// 31: 274-295. [[http://adn.biol.umontreal.ca/~numericalecology/Reprints/Murtagh_Legendre_J_Class_2014.pdf|pdf]]
  * Murtaugh, P.A. 2014. In defence of //P// values. //Ecology// 95: 611-617. https://doi.org/10.1890/13-0590.1 [[http://www.science.oregonstate.edu/~murtaugp/files/ecol-2014.pdf|pdf]]
  * Oksanen, J. (2015) //Multivariate Analysis of Ecological Communities in R: vegan tutorial//. [[http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf|pdf]]
  * Peres-Neto, P.R., Jackson, D.A. & Somers, K.M. 2005. How many principal components? Stopping rules for determining the number of non-trivial axes revisited. //Computational Statistics & Data Analysis// 49:974–997.[[http://www.er.uqam.ca/nobel/r3424621/labo/fr/site/Pedro_files/how%20many%20principal%20components.pdf|pdf]]
  * Peres-Neto, P.R., Legendre, P., Dray, S. & Borcard, D. 2006. Variation partitioning of species data matrices: estimation and comparison of fractions. //Ecology// 87:2614–2625. [[http://adn.biol.umontreal.ca/~numericalecology/Reprints/Peres-Neto_et_al_2006_with_app.pdf|pdf]]
  * Smith, T.W. & Lundholm, J.T. 2010. Variation partitioning as a tool to distinguish between niche and neutral processes. //Ecography// 33: 648-655. [[http://www.researchgate.net/publication/229492244_Variation_partitioning_as_a_tool_to_distinguish_between_niche_and_neutral_processes/file/504635176953a43056.pdf|pdf]]
  * Šmilauer, P. & Lepš, J. 2014. //Multivariate Analysis of Ecological Data using Canoco 5.// Second Edition. Cambridge University Press, Cambridge, UK.
  * ter Braak, C.J.F. 1986. Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. //Ecology// 67: 1167-1179. [[https://www.uprm.edu/biology/profs/chinea/comunidades/refs/ter_braak1986.pdf|pdf]]
  * ter Braak, C.J.F. & Šmilauer, P. 2002. //CANOCO Reference Manual and CanodDraw for Windows User's Guide: Software for Canonical Community Ordination (version 4.5.)//. Microcomputer Power, New York.
  * ter Braak, C.J.F. & Šmilauer, P. 2012. //CANOCO Reference Manual and User's Guide: Software for Ordination (version 5.0)//. Microcomputer Power (Ithaca, NY, USA), 496 pp.
  * ter Braak, C.J.F. & Šmilauer, P. 2015. Topics in constrained and unconstrained ordination. //Plant Ecology// 216: 683–696. https://doi.org/10.1007/s11258-014-0356-5 [[http://edepot.wur.nl/323327|pdf]]
  * Tukey, J.W. 1980. We need both exploratory and confirmatory. The American Statistician, 34, 23-25. {{ :en:papers:tukey1980_amer-stat.pdf|pdf}}
  * Whittaker, R.H. 1960. Vegetation of the Siskiyou Mountains, Oregon and California. //Ecological Monographs// 30: 279-338. [[http://www.thesfi.org/Files/Whittaker%201960.pdf|pdf]]
  * Wilson, J.B. 2012. Species presence/absence sometimes represents a plant community as well as species abundances do, or better. //Journal of Vegetation Science// 23: 1013–1023.  https://doi.org/10.1111/j.1654-1103.2012.01430.x
  * Zuur A.F., Ieno E.N. & Smith G.M. 2007. //Analysing ecological data//. New York. Springer.
Analysis of community ecology data in R

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