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The ecodist Package for Dissimilarity-based Analysis of Ecological Data

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  • Goslee, Sarah C.
  • Urban, Dean L.

Abstract

Ecologists are concerned with the relationships between species composition and environmental framework incorporating space explicitly is an extremely flexible tool for answering these questions. The R package ecodist brings together methods for working with dissimilarities, including some not available in other R packages. We present some of the features of ecodist, particularly simple and partial Mantel tests, and make recommendations for their effective use. Although the partial Mantel test is often used to account for the effects of space, the assumption of linearity greatly reduces its effectiveness for complex spatial patterns. We introduce a modification of the Mantel correlogram designed to overcome this restriction and allow consideration of complex nonlinear structures. This extension of the method allows the use of partial multivariate correlograms and tests of relationship between variables at different spatial scales. Some of the possibilities are demonstrated using both artificial data and data from an ongoing study of plant community composition in grazinglands of the northeastern United States.

Suggested Citation

  • Goslee, Sarah C. & Urban, Dean L., 2007. "The ecodist Package for Dissimilarity-based Analysis of Ecological Data," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i07).
    • Handle: RePEc:jss:jstsof:v:022:i07
    DOI: http://hdl.handle.net/10.18637/jss.v022.i07
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    References listed on IDEAS

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    1. Reik Oberrath & Katrin Bohning-Gaese, 2001. "The Signed Mantel test to cope with autocorrelation in comparative analyses," Journal of Applied Statistics, Taylor & Francis Journals, vol. 28(6), pages 725-736.
    2. Neal Oden & Robert Sokal, 1992. "An investigation of three-matrix permutation tests," Journal of Classification, Springer;The Classification Society, vol. 9(2), pages 275-290, December.
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    Cited by:

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    2. Annika Busse & Pablo A P Antiqueira & Alexandre S Neutzling & Anna M Wolf & Gustavo Q Romero & Jana S Petermann, 2018. "Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna," PLOS ONE, Public Library of Science, vol. 13(2), pages 1-20, February.
    3. Benoit Talbot & Dany Garant & Sébastien Rioux Paquette & Julien Mainguy & Fanie Pelletier, 2012. "Lack of Genetic Structure and Female-Specific Effect of Dispersal Barriers in a Rabies Vector, the Striped Skunk (Mephitis mephitis)," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-7, November.
    4. Ekaterina Dolbunova & Alexandre Lucquin & T. Rowan McLaughlin & Manon Bondetti & Blandine Courel & Ester Oras & Henny Piezonka & Harry K. Robson & Helen Talbot & Kamil Adamczak & Konstantin Andreev & , 2023. "The transmission of pottery technology among prehistoric European hunter-gatherers," Nature Human Behaviour, Nature, vol. 7(2), pages 171-183, February.
    5. Eric Vander Wal & Audrey Gagné-Delorme & Marco Festa-Bianchet & Fanie Pelletier, 2016. "Dyadic associations and individual sociality in bighorn ewes," Behavioral Ecology, International Society for Behavioral Ecology, vol. 27(2), pages 560-566.
    6. Wilson Lara & Stella Bogino & Felipe Bravo, 2018. "Multilevel analysis of dendroclimatic series with the R-package BIOdry," PLOS ONE, Public Library of Science, vol. 13(5), pages 1-23, May.
    7. Turner, Rachel A. & Polunin, Nicholas V.C. & Stead, Selina M., 2015. "Mapping inshore fisheries: Comparing observed and perceived distributions of pot fishing activity in Northumberland," Marine Policy, Elsevier, vol. 51(C), pages 173-181.
    8. Kraker, Peter & Schlögl, Christian & Jack, Kris & Lindstaedt, Stefanie, 2015. "Visualization of co-readership patterns from an online reference management system," Journal of Informetrics, Elsevier, vol. 9(1), pages 169-182.
    9. Anna C. Peterson & Himanshu Sharma & Arvind Kumar & Bruno M. Ghersi & Scott J. Emrich & Kurt J. Vandegrift & Amit Kapoor & Michael J. Blum, 2021. "Rodent Virus Diversity and Differentiation across Post-Katrina New Orleans," Sustainability, MDPI, vol. 13(14), pages 1-18, July.
    10. Ishrat Z. Anka & Tamsyn M. Uren Webster & Waldir M. Berbel-Filho & Matthew Hitchings & Benjamin Overland & Sarah Weller & Carlos Garcia de Leaniz & Sofia Consuegra, 2024. "Microbiome and epigenetic variation in wild fish with low genetic diversity," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    11. Charles Cunningham & Jorge E Parra & Lucy Coals & Marcela Beltrán & Sama Zefania & Tamás Székely, 2018. "Social interactions predict genetic diversification: an experimental manipulation in shorebirds," Behavioral Ecology, International Society for Behavioral Ecology, vol. 29(3), pages 609-618.
    12. Davide Rassati & Massimo Faccoli & Robert A Haack & Robert J Rabaglia & Edoardo Petrucco Toffolo & Andrea Battisti & Lorenzo Marini, 2016. "Bark and Ambrosia Beetles Show Different Invasion Patterns in the USA," PLOS ONE, Public Library of Science, vol. 11(7), pages 1-17, July.
    13. Michael F Bonner & Russell A Epstein, 2018. "Computational mechanisms underlying cortical responses to the affordance properties of visual scenes," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-31, April.
    14. Emily, Mathieu & Hitte, Christophe & Mom, Alain, 2016. "SMILE: A novel dissimilarity-based procedure for detecting sparse-specific profiles in sparse contingency tables," Computational Statistics & Data Analysis, Elsevier, vol. 99(C), pages 171-188.
    15. Lucas P. Martins & Daniel B. Stouffer & Pedro G. Blendinger & Katrin Böhning-Gaese & Galo Buitrón-Jurado & Marta Correia & José Miguel Costa & D. Matthias Dehling & Camila I. Donatti & Carine Emer & M, 2022. "Global and regional ecological boundaries explain abrupt spatial discontinuities in avian frugivory interactions," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    16. repec:jss:jstsof:31:i03 is not listed on IDEAS
    17. R. Bhalla & Neil Pelkey & K. Devi Prasad, 2011. "Application of GIS for Evaluation and Design of Watershed Guidelines," Water Resources Management: An International Journal, Published for the European Water Resources Association (EWRA), Springer;European Water Resources Association (EWRA), vol. 25(1), pages 113-140, January.
    18. Samantha Bothwell & Alex Kaizer & Ryan Peterson & Danielle Ostendorf & Victoria Catenacci & Julia Wrobel, 2023. "Pattern‐based clustering of daily weigh‐in trajectories using dynamic time warping," Biometrics, The International Biometric Society, vol. 79(3), pages 2719-2731, September.
    19. repec:jss:jstsof:22:i01 is not listed on IDEAS
    20. Kneib, Thomas & Petzoldt, Thomas, 2007. "Introduction to the Special Volume on "Ecology and Ecological Modeling in R"," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i01).
    21. Pebesma, Edzer & Bivand, Roger & Ribeiro, Paulo Justiniano, 2015. "Software for Spatial Statistics," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i01).

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