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The ade4 Package: Implementing the Duality Diagram for Ecologists
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Multivariate analyses are well known and widely used to identify and understand structures of ecological communities. The ade4 package for the R statistical environment proposes a great number of multivariate methods. Its implementation follows the tradition of the French school of
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Cites
Ecologically meaningful transformations for ordination of species data
Legendre, P., & Gallagher, E. D. (2001) · Oecologia · doi:10.1007/s004420100716 · Cited by 5,556
Cited by
Enterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548
Kowal, J., Arras, G., Colombo, M., Jouve, M., Morath, J. P., Primdal-Bengtson, B., Dingli, F., Loew, D., Tkach, M., & Théry, C. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521230113 · Cited by 3,426
Symptomatic atherosclerosis is associated with an altered gut metagenome
Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012) · Nature Communications · doi:10.1038/ncomms2266 · Cited by 1,371
Fourcade, Y., Engler, J. O., Rödder, D., & Secondi, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097122 · Cited by 1,098
Undulating changes in human plasma proteome profiles across the lifespan
Lehallier, B., Gate, D., Schaum, N., Nanasi, T., Lee, S. E., Yousef, H., Moran Losada, P., Berdnik, D., Keller, A., Verghese, J., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0673-2 · Cited by 981
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents
Hoffmann, C., Dollive, S., Grunberg, S., Chen, J., Li, H., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066019 · Cited by 808
Land-use intensification causes multitrophic homogenization of grassland communities
Gossner, M. M., Lewinsohn, T. M., Kahl, T., Grassein, F., Boch, S., Prati, D., Birkhofer, K., Renner, S. C., Sikorski, J., Wubet, T., et al. (2016) · Nature · doi:10.1038/nature20575 · Cited by 706
Segal, L. N., Alekseyenko, A. V., Clemente, J. C., Kulkarni, R., Wu, B., Chen, H., Berger, K. I., Goldring, R. M., Rom, W. N., Blaser, M. J., et al. (2013) · Microbiome · doi:10.1186/2049-2618-1-19 · Cited by 482
Breast cancer in postmenopausal women is associated with an altered gut metagenome
Zhu, J., Liao, M., Yao, Z., Liang, W., Li, Q., Liu, J., Yang, H., Ji, Y., Wei, W., Tan, A., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0515-3 · Cited by 377
Dzidic, M., Collado, M. C., Abrahamsson, T., Artacho, A., Stensson, M., Jenmalm, M. C., & Mira, A. (2018) · The ISME Journal · doi:10.1038/s41396-018-0204-z · Cited by 279
Llorente, C., Jepsen, P., Inamine, T., Wang, L., Bluemel, S., Wang, H. J., Loomba, R., Bajaj, J. S., Schubert, M. L., Sikaroodi, M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00796-x · Cited by 257
Integrative modeling of gene and genome evolution roots the archaeal tree of life
Williams, T. A., Szöllősi, G. J., Spang, A., Foster, P. G., Heaps, S. E., Boussau, B., Ettema, T. J. G., & Embley, T. M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618463114 · Cited by 233
Zinkernagel, M. S., Zysset-Burri, D. C., Keller, I., Berger, L. E., Leichtle, A. B., Largiadèr, C. R., Fiedler, G. M., & Wolf, S. (2017) · Scientific Reports · doi:10.1038/srep40826 · Cited by 229
Cronin, O., Barton, W., Skuse, P., Penney, N. C., Garcia-Perez, I., Murphy, E. F., Woods, T., Nugent, H., Fanning, A., Melgar, S., et al. (2018) · mSystems · doi:10.1128/msystems.00044-18 · Cited by 232
Tran, T. T. T., Corsini, S., Kellingray, L., Hegarty, C., Le Gall, G., Narbad, A., Müller, M., Tejera, N., O'Toole, P. W., Minihane, A.-M., et al. (2019) · The FASEB Journal · doi:10.1096/fj.201900071r · Cited by 233
A new species of Homo from the Late Pleistocene of the Philippines
Détroit, F., Mijares, A. S., Corny, J., Daver, G., Zanolli, C., Dizon, E., Robles, E., Grün, R., & Piper, P. J. (2019) · Nature · doi:10.1038/s41586-019-1067-9 · Cited by 230
Perović, D., Gámez‐Virués, S., Börschig, C., Klein, A., Krauss, J., Steckel, J., Rothenwöhrer, C., Erasmi, S., Tscharntke, T., & Westphal, C. (2015) · Journal of Applied Ecology · doi:10.1111/1365-2664.12394 · Cited by 189
Autism traits in the RASopathies
Adviento, B., Corbin, I. L., Widjaja, F., Desachy, G., Enrique, N., Rosser, T., Risi, S., Marco, E. J., Hendren, R. L., Bearden, C. E., et al. (2014) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2013-101951 · Cited by 174
Mathur, V., Burai, R., Vest, R. T., Bonanno, L. N., Lehallier, B., Zardeneta, M. E., Mistry, K. N., Do, D., Marsh, S. E., Abud, E. M., et al. (2017) · Neuron · doi:10.1016/j.neuron.2017.11.032 · Cited by 175
Exploration of bacterial community classes in major human habitats
Zhou, Y., Mihindukulasuriya, K. A., Gao, H., La Rosa, P. S., Wylie, K. M., Martin, J. C., Kota, K., Shannon, W. D., Mitreva, M., Sodergren, E., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-5-r66 · Cited by 149
Kaya, C., Generalovic, T. N., Ståhls, G., Hauser, M., Samayoa, A. C., Nunes-Silva, C. G., Roxburgh, H., Wohlfahrt, J., Ewusie, E. A., Kenis, M., et al. (2021) · BMC Biology · doi:10.1186/s12915-021-01029-w · Cited by 149
Cadière, A., Ortiz-Julien, A., Camarasa, C., & Dequin, S. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.01.008 · Cited by 141
The best practice for microbiome analysis using R
Wen, T., Niu, G., Chen, T., Shen, Q., Yuan, J., & Liu, Y.-X. (2023) · Protein & Cell · doi:10.1093/procel/pwad024 · Cited by 139
A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow
Proctor, D. M., Fukuyama, J. A., Loomer, P. M., Armitage, G. C., Lee, S. A., Davis, N. M., Ryder, M. I., Holmes, S. P., & Relman, D. A. (2018) · Nature Communications · doi:10.1038/s41467-018-02900-1 · Cited by 115
Potential adaptive strategies for 29 sub-Saharan crops under future climate change
Pironon, S., Etherington, T. R., Borrell, J. S., Kühn, N., Macias-Fauria, M., Ondo, I., Tovar, C., Wilkin, P., & Willis, K. J. (2019) · Nature Climate Change · doi:10.1038/s41558-019-0585-7 · Cited by 116
Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus
Sewell, T. R., Zhu, J., Rhodes, J., Hagen, F., Meis, J. F., Fisher, M. C., & Jombart, T. (2019) · mBio · doi:10.1128/mbio.00392-19 · Cited by 109
Zysset-Burri, D. C., Keller, I., Berger, L. E., Largiadèr, C. R., Wittwer, M., Wolf, S., & Zinkernagel, M. S. (2020) · npj Genomic Medicine · doi:10.1038/s41525-020-00141-0 · Cited by 94
Balaresque, P., Poulet, N., Cussat-Blanc, S., Gerard, P., Quintana-Murci, L., Heyer, E., & Jobling, M. A. (2015) · European Journal of Human Genetics · doi:10.1038/ejhg.2014.285 · Cited by 89
Functional trait differences influence neighbourhood interactions in a hyperdiverse Amazonian forest
Fortunel, C., Valencia, R., Wright, S. J., Garwood, N. C., & Kraft, N. J. B. (2016) · Ecology Letters · doi:10.1111/ele.12642 · Cited by 83
Kantar, M. B., Sosa, C. C., Khoury, C. K., Castañeda-Álvarez, N. P., Achicanoy, H. A., Bernau, V., Kane, N. C., Marek, L., Seiler, G., & Rieseberg, L. H. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00841 · Cited by 76
Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species
Wells, K., Morand, S., Wardeh, M., & Baylis, M. (2020) · Global Ecology and Biogeography · doi:10.1111/geb.13045 · Cited by 65
Rarity, trophy hunting and ungulates
Palazy, L., Bonenfant, C., Gaillard, J. M., & Courchamp, F. (2012) · Animal Conservation · doi:10.1111/j.1469-1795.2011.00476.x · Cited by 69
Mbole-Kariuki, M. N., Sonstegard, T., Orth, A., Thumbi, S. M., Bronsvoort, B. M. D. C., Kiara, H., Toye, P., Conradie, I., Jennings, A., Coetzer, K., et al. (2014) · Heredity · doi:10.1038/hdy.2014.31 · Cited by 69
Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank
Leite, M. F. A., Pan, Y., Bloem, J., Berge, H. T., & Kuramae, E. E. (2017) · Scientific Reports · doi:10.1038/srep42634 · Cited by 63
Exploring the reservoir of potential fungal plant pathogens in agricultural soil
Agtmaal, M. V., Straathof, A., Termorshuizen, A., Teurlincx, S., Hundscheid, M., Ruyters, S., Busschaert, P., Lievens, B., & Boer, W. D. (2017) · Applied Soil Ecology · doi:10.1016/j.apsoil.2017.09.032 · Cited by 62
Importance of spatio–temporal connectivity to maintain species experiencing range shifts
Huang, J., Andrello, M., Martensen, A. C., Saura, S., Liu, D., He, J., & Fortin, M. (2020) · Ecography · doi:10.1111/ecog.04716 · Cited by 62
Gravel dredging alters diversity and structure of riverine fish assemblages
FREEDMAN, J. A., CARLINE, R. F., & STAUFFER, J. R. (2013) · Freshwater Biology · doi:10.1111/fwb.12056 · Cited by 62
Modularity as a source of new morphological variation in the mandible of hybrid mice
Renaud, S., Alibert, P., & Auffray, J.-C. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-141 · Cited by 51
Elbrecht, V., Feld, C. K., Gies, M., Hering, D., Sondermann, M., Tollrian, R., & Leese, F. (2014) · Freshwater Science · doi:10.1086/674536 · Cited by 49
An altered fecal microbial profiling in rosacea patients compared to matched controls
Chen, Y.-J., Lee, W.-H., Ho, H. J., Tseng, C.-H., & Wu, C.-Y. (2021) · Journal of the Formosan Medical Association · doi:10.1016/j.jfma.2020.04.034 · Cited by 46
Cadière, A., Aguera, E., Caillé, S., Ortiz-Julien, A., & Dequin, S. (2012) · Food Microbiology · doi:10.1016/j.fm.2012.07.010 · Cited by 41
Thoumazeau, A., Bessou, C., Renevier, M.-S., Panklang, P., Puttaso, P., Peerawat, M., Heepngoen, P., Polwong, P., Koonklang, N., Sdoodee, S., et al. (2019) · Ecological Indicators · doi:10.1016/j.ecolind.2018.10.028 · Cited by 39
Sex‐specific genetic diversity is shaped by cultural factors in Inner Asian human populations
Marchi, N., Hegay, T., Mennecier, P., Georges, M., Laurent, R., Whitten, M., Endicott, P., Aldashev, A., Dorzhu, C., Nasyrova, F., et al. (2017) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23151 · Cited by 38
Vanwindekens, F. M., Baret, P. V., & Stilmant, D. (2014) · Ecological Modelling · doi:10.1016/j.ecolmodel.2013.11.026 · Cited by 34
Sargis, E. J., Millien, V., Woodman, N., & Olson, L. E. (2018) · Ecology and Evolution · doi:10.1002/ece3.3682 · Cited by 32
Basto, M. P., Santos-Reis, M., Simões, L., Grilo, C., Cardoso, L., Cortes, H., Bruford, M. W., & Fernandes, C. (2016) · PLOS ONE · doi:10.1371/journal.pone.0145165 · Cited by 28
Community assembly, functional traits, and phylogeny in Himalayan river birds
Sinha, A., Chatterjee, N., Krishnamurthy, R., & Ormerod, S. J. (2022) · Ecology and Evolution · doi:10.1002/ece3.9012 · Cited by 21
“…across river reaches surveyed as 15 species abundances*68 sites), R (environmental characteristics of samples: 68 sites*12 environmental variables), and Q (species traits: 15 species*8 traits) were analyzed separately using different ordination methods in “ade4” package in R (Dray & Dufour, 2007).”
MethodFeng, S., Guo, L., Wang, H., Yang, S., & Liu, H. (2023) · Communications Biology · doi:10.1038/s42003-023-04613-8 · Cited by 20
Biryol, C., Aupic‐Samain, A., Lecareux, C., Gauquelin, T., Baldy, V., & Santonja, M. (2024) · Oikos · doi:10.1111/oik.10345 · Cited by 12
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Hendier, A., Chatelain, C., Du Pasquier, P., Paris, M., Ouattara, K., Koné, I., Croll, D., & Zuberbühler, K. (2021) · African Journal of Ecology · doi:10.1111/aje.12888 · Cited by 7
Tarkhnishvili, D., Gavashelishvili, A., Murtskhvaladze, M., & Latsuzbaia, A. (2016) · Human Biology · doi:10.13110/humanbiology.88.4.0287 · Cited by 7
Ruge, J., Ehlers, M. R., Kastrinogiannis, A., Klingelhöfer-Jens, M., Koppold, A., Abend, R., & Lonsdorf, T. B. (2023) · doi:10.31234/osf.io/nfpbj · Cited by 7
Metadata
- Authors
- Dray, S., & Dufour, A.-B.
- Venue
- Journal of Statistical Software
- Publisher
- Foundation for Open Access Statistic
- Published
- 2007
- Volume
- 22
- Issue
- 4
- ISSN
- 1548-7660 (ISSN-L)
- OpenAlex
- W2130517250
- Cited by
- 6,211
- References
- 1
- FWCI
- 44.52
- Type
- journal article
- Language
- en
- Open access
- diamond
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