<script src="https://bibbase.org/mendeley2/2845861?jsonp=1"></script>
<?php
$contents = file_get_contents("https://bibbase.org/mendeley2/2845861");
print_r($contents);
?>
<iframe src="https://bibbase.org/mendeley2/2845861"></iframe>
For more details see the documention.
To the site owner:
Action required! Mendeley is changing its API. In order to keep using Mendeley with BibBase past April 14th, you need to:
@article{ title = {Heterogeneity of water physico-chemical characteristics in artificially pumped waterholes: do African herbivores drink at the same locations and does it lead to interference competition?}, type = {article}, year = {2020}, keywords = {Interference competition,Large African herbivores,Resource quality heterogeneity,Semi-arid savanna,Spatial aggregation,Waterhole scale}, pages = {104014}, volume = {173}, websites = {https://doi.org/10.1016/j.jaridenv.2019.104014}, publisher = {Elsevier}, id = {1c3a3d2d-681f-31d0-a781-baa5a5681ec9}, created = {2019-11-06T18:43:24.165Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:54:57.311Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Ferry2020}, private_publication = {false}, bibtype = {article}, author = {Ferry, Nicolas and Cordonnier, Marion and Hulot, Florence D and Dakwa, Farisayi and Sebele, Lovelater and Dray, Stéphane and Fritz, Hervé and Valeix, Marion}, doi = {10.1016/j.jaridenv.2019.104014}, journal = {Journal of Arid Environments}, number = {August 2019} }
@article{ title = {Flower phenology as a disruptor of the fruiting dynamics in temperate oak species}, type = {article}, year = {2020}, keywords = {masting,oak species,pollen phenology,resource budget model,stochastic mast seeding}, id = {9a4e36b2-d4d1-38bb-8041-501aaccb57bf}, created = {2020-01-29T13:05:12.634Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:56:10.316Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {false}, hidden = {false}, citation_key = {Schermer2019}, private_publication = {false}, abstract = {Many perennial plants display masting, that is, fruiting with strong interannual variations, irregular and synchronized between trees within the population. Here, we tested the hypothesis that the early flower phenology in temperate oak species promotes stochasticity into their fruiting dynamics, which could play a major role in tree reproductive success. From a large field monitoring network, we compared the pollen phenology between temperate and Mediterranean oak species. Then, focusing on temperate oak species, we explored the influence of the weather around the time of budburst and flowering on seed production, and simulated with a mechanistic model the consequences that an evolutionary shifting of flower phenology would have on fruiting dynamics. Temperate oak species release pollen earlier in the season than do Mediterranean oak species. Such early flowering in temperate oak species results in pollen often being released during unfavorable weather conditions and frequently results in reproductive failure. If pollen release were delayed as a result of natural selection, fruiting dynamics would exhibit much reduced stochastic variation. We propose that early flower phenology might be adaptive by making mast-seeding years rare and unpredictable, which would greatly help in controlling the dynamics of seed consumers.}, bibtype = {article}, author = {Schermer, Éliane and Bel-Venner, Marie Claude and Gaillard, Jean Michel and Dray, Stéphane and Boulanger, Vincent and Le Roncé, Iris and Oliver, Gilles and Chuine, Isabelle and Delzon, Sylvain and Venner, Samuel}, doi = {10.1111/nph.16224}, journal = {New Phytologist} }
@article{ title = {Investigating microbial associations from sequencing survey data with co-correspondence analysis}, type = {article}, year = {2020}, keywords = {Mamiellophyceae,Prasinovirus,co-correspondence analysis,co-occurrence network,microbial eukaryotes,next-generation sequencing}, pages = {468-480}, volume = {20}, id = {ed1af254-957b-342d-b4cc-550a623f40da}, created = {2020-01-29T13:05:12.754Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:55:58.094Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Alric2020}, private_publication = {false}, abstract = {Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next-generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co-correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co-occurrence networks and thus investigate the presence of patterns in ecological networks.}, bibtype = {article}, author = {Alric, Benjamin and ter Braak, Cajo J.F. and Desdevises, Yves and Lebredonchel, Hugo and Dray, Stéphane}, doi = {10.1111/1755-0998.13126}, journal = {Molecular Ecology Resources} }
@article{ title = {Diversity indices for ecological networks: a unifying framework using Hill numbers}, type = {article}, year = {2019}, keywords = {hill numbers,interaction network diversity,metanetwork,species aggregation level}, pages = {737-747}, volume = {22}, id = {552a9b7d-b85f-39e6-89d3-f39e9b670146}, created = {2019-02-26T16:45:21.004Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:53:30.804Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Ohlmann2019}, private_publication = {false}, abstract = {Describing how ecological interactions change over space and time and how they are shaped by environmental conditions is crucial to understand and predict ecosystem trajectories. However, it requires having an appropriate framework to measure network diversity locally, regionally and between samples (α‐, γ‐ and β‐diversity). Here, we propose a unifying framework that builds on Hill numbers and accounts both for the probabilistic nature of biotic interactions and the abundances of species or groups. We emphasise the importance of analysing network diversity across different species aggregation levels (e.g. from species to trophic groups) to get a better understanding of network structure. We illustrate our framework with a simulation experiment and an empirical analysis using a global food‐web database. We discuss further usages of the framework and show how it responds to recent calls on comparing ecological networks and analysing their variation across environmental gradients and time.}, bibtype = {article}, author = {Ohlmann, Marc and Miele, Vincent and Dray, Stéphane and Chalmandrier, Loïc and O’Connor, Louise and Thuiller, Wilfried}, doi = {10.1111/ele.13221}, journal = {Ecology Letters} }
@article{ title = {Testing the Mantel statistic with a spatially-constrained permutation procedure}, type = {article}, year = {2019}, keywords = {Mantel test,Moran spectral randomization,distance decay relationships,principal coordinates analysis,spatial autocorrelation,spatially constrained null model,type I error inflation}, pages = {532-540}, volume = {10}, id = {ad145f1c-5ea6-3112-a83c-db71e010f148}, created = {2019-02-26T16:45:21.006Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:53:42.188Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Crabot2019}, private_publication = {false}, abstract = {Mantel tests are widely used in ecology to assess the significance of the relationship between two distance matrices computed between pairs of samples. However, recent studies demonstrated that the presence of spatial autocorrelation in both distance matrices induced inflations of parameter estimates and type I error rates. These results also hold for partial Mantel test which is supposed to control for the spatial structures. To address the issue of spatial autocorrelation in testing the Mantel statistic, we developed a new procedure based on spatially constrained randomizations using Moran spectral randomization. A simulation study was conducted to assess the performance of this new procedure. Different scenarios were considered by manipulating the number of variables, the number of samples, the regularity of the sampling design and the level of spatial autocorrelation. As identified by previous studies, we found that Mantel statistic and its associated type I error rate are inflated in simple and partial Mantel tests when both distances matrices are spatially structured. We showed that these biases increased with the number of variables, decreased with the number of samples and were slightly lower for regular than irregular sampling. The new procedure succeeded in correcting the spurious inflations of the parameter estimates and type I error rates in any of the presented scenarios. Our results suggest that studies from several fields (e.g. genetic or community ecology) could have been overestimating the relationship between two distances matrices when both presented spatial autocorrelation. We proposed an alternative solution applicable in every field to correctly compute Mantel statistic with a fair type I error rate.}, bibtype = {article}, author = {Crabot, Julie and Clappe, Sylvie and Dray, Stéphane and Datry, Thibault}, doi = {10.1111/2041-210X.13141}, journal = {Methods in Ecology and Evolution} }
@article{ title = {Spatial analyses of multi‐trophic terrestrial vertebrate assemblages in Europe}, type = {article}, year = {2019}, keywords = {biodiversity,environmental gradients,food web comparison,metaweb,network properties,null model,tetrapod communities}, pages = {1636-1648}, volume = {28}, id = {6dfed49b-eae8-3517-bf85-a10780229bf9}, created = {2019-10-18T11:42:24.370Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:54:31.091Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Braga2019}, private_publication = {false}, bibtype = {article}, author = {Braga, João and Pollock, Laura J. and Barros, Ceres and Galiana, Núria and Montoya, José M. and Gravel, Dominique and Maiorano, Luigi and Montemaggiori, Alessandro and Ficetola, Gentile Francesco and Dray, Stéphane and Thuiller, Wilfried}, doi = {10.1111/geb.12981}, journal = {Global Ecology and Biogeography} }
@inproceedings{ title = {Analyse des structures spatiales multivariées en écologie des communautés avec le package adespatial}, type = {inproceedings}, year = {2019}, city = {Nantes, France}, id = {4d8e399c-0fe6-3321-b74c-6c4368c79fb7}, created = {2020-01-29T13:05:12.671Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-01-29T13:05:12.671Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2019d}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {JIEM} }
@inproceedings{ title = {Moran eigenvector filters for the analysis of ecological data : are they really multiscale?}, type = {inproceedings}, year = {2019}, city = {Saclay, France}, id = {285f7212-4ed2-301e-a1e9-ae8e1a27a727}, created = {2020-01-29T13:05:12.672Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-01-29T13:05:12.672Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2019c}, notes = {Invited conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Ecosystems Dynamics} }
@inproceedings{ title = {Portail web pour soumettre, formater et partager des jeux de données dans R}, type = {inproceedings}, year = {2019}, city = {Lyon, France}, id = {56cd631b-e5c2-3126-badb-6a981718e4a6}, created = {2020-01-29T13:05:12.725Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-01-29T13:05:12.725Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2019b}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Journée du réseau ARAMIS, 23 May} }
@inproceedings{ title = {How to deal with missing and confounding variables in multivariate analysis?}, type = {inproceedings}, year = {2019}, city = {Aix-en-Provence, France}, id = {f2b86703-1160-3816-a770-78c1ce38f4e0}, created = {2020-01-29T13:05:12.727Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-01-29T13:05:12.727Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2019a}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Séminaire scientifique annuel du SRTE, 25 September} }
@article{ title = {Phenotypic plasticity in the invasive pest Drosophila suzukii: Activity rhythms and gene expression in response to temperature}, type = {article}, year = {2019}, keywords = {Circadian rhythm,Clock genes,Drosophila melanogaster,Drosophila suzukii,Functional principal component analysis,Invasion biology}, volume = {222}, id = {9f07d619-3b1d-311e-84ca-ebd8e9f90e14}, created = {2020-01-29T13:05:12.758Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:55:38.984Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Plantamp2019}, private_publication = {false}, abstract = {Phenotypic plasticity may contribute to the invasive success of an alien species in a new environment. A highly plastic species may survive and reproduce in more diverse environments, thereby supporting establishment and colonization. We focused on plasticity in the circadian rhythm of activity, which can favour species coexistence in invasion, for the invasive species Drosophila suzukii, which is expected to be a weaker direct competitor than other Drosophila species of the resident community. We compared the circadian rhythms of the locomotor activity in adults and the expression of clock genes in response to temperature in the invasive D. suzukii and the resident Drosophila melanogaster. We showed that D. suzukii is active in a narrower range of temperatures than D. melanogaster and that the activities of the two species overlap during the day, regardless of the temperature. Both species are diurnal and exhibit rhythmic activity at dawn and dusk, with a much lower activity at dawn for D. suzukii females. Our results show that the timeless and clock genes are good candidates to explain the plastic response that is observed in relation to temperature. Overall, our results suggest that thermal phenotypic plasticity in D. suzukii activity is not sufficient to explain the invasive success of D. suzukii and call for testing other hypotheses, such as the release of competitors and/or predators.}, bibtype = {article}, author = {Plantamp, Christophe and Henri, Hélène and Andrieux, Thibault and Régis, Corinne and Mialdea, Gladys and Dray, Stéphane and Gibert, Patricia and Desouhant, Emmanuel}, doi = {10.1242/jeb.199398}, journal = {Journal of Experimental Biology}, number = {14} }
@article{ title = {Nine quick tips for analyzing network data}, type = {article}, year = {2019}, pages = {1-10}, volume = {15}, id = {5fd19426-338e-3965-9aec-34f0fd6ac4f6}, created = {2020-01-29T13:05:12.779Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:55:46.478Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Miele2019}, private_publication = {false}, bibtype = {article}, author = {Miele, Vincent and Matias, Catherine and Robin, Stéphane and Dray, Stéphane}, doi = {10.1371/journal.pcbi.1007434}, journal = {PLoS Computational Biology}, number = {12} }
@article{ title = {Disentangling good from bad practices in the selection of spatial or phylogenetic eigenvectors}, type = {article}, year = {2018}, keywords = {Akaike information criterion (AIC),Ecological processes,Eigenvector selection,Forward selection,Moran's eigenvector maps (MEM),Phylogenetic eigenvector regression (PVR),Principal coordinates of neighbour matrices (PCNM),Spatial eigenvector mapping (SEVM),Spatial patterns,Variation partitioning}, pages = {1638-1649}, volume = {41}, id = {1dd15bfc-5672-3650-8a30-231666f2f869}, created = {2018-02-22T01:15:09.173Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:49:03.552Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Bauman2018}, private_publication = {true}, abstract = {Eigenvector mapping techniques are widely used by ecologists and evolutionary biologists to describe and control for spatial and/or phylogenetic patterns in their data. The selection of an appropriate subset of eigenvectors is a critical step (misspecification can lead to highly biased results and interpretations), and there is no consensus yet on how to proceed. We conducted a ten‐year review of the practices of eigenvector selection and highlighted three main procedures: selecting the subset of descriptors minimising the Akaike information criterion (AIC), using a forward selection with double stopping criterion after testing the global model significance (FWD), and selecting the subset minimising the autocorrelation in the model residuals (MIR). We compared the type I error rates, statistical power, and R² estimation accuracy of these methods using simulated data. Finally, a real dataset was analysed using variation partitioning analysis to illustrate to what extent the different selection approaches affected the ecological interpretation of the results. We show that, while the FWD and MIR approaches presented a correct type I error rate and were accurate, the AIC approach displayed extreme type I error rates (100%), and strongly overestimated the R². Moreover, the AIC approach resulted in wrong ecological interpretations, as it overestimated the pure spatial fraction (and the joint spatial‐environmental fraction to a lesser extent) of the variation partitioning. Both the FWD and MIR methods performed well at broad and medium scales but had a very low power to detect fine‐scale patterns. The FWD approach selected more eigenvectors than the MIR approach but also returned more accurate R² estimates. Hence, we discourage any future use of the AIC approach, and advocate choosing between the MIR and FWD approaches depending on the objective of the study: controlling for spatial or phylogenetic autocorrelation (MIR) or describing the patterns as accurately as possible (FWD).}, bibtype = {article}, author = {Bauman, David and Drouet, Thomas and Dray, Stéphane and Vleminckx, Jason}, doi = {10.1111/ecog.03380}, journal = {Ecography} }
@article{ title = {Algorithms and biplots for double constrained correspondence analysis}, type = {article}, year = {2018}, keywords = {Biplot,Canonical correlation analysis,Canonical correspondence analysis,Community ecology,Fourth-corner correlation,Multivariate analysis,Trait-environment relations}, pages = {171-197}, volume = {25}, websites = {https://doi.org/10.1007/s10651-017-0395-x}, publisher = {Springer US}, id = {f67d5fb3-716e-3ee9-a73c-d4a65dc112fa}, created = {2018-05-28T10:13:35.807Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2018-05-28T10:14:12.242Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {TerBraak2018}, private_publication = {false}, abstract = {Correspondence analysis with linear external constraints on both the rows and the columns has been mentioned in the ecological literature, but lacks full mathematical treatment and easily available algorithms and software. This paper fills this gap by defining the method as maximizing the fourth-corner correlation between linear combinations, by providing novel algorithms, which demonstrate relationships with related methods, and by making a detailed study of possible biplots and associated approximations. The method is illustrated using ecological data on the abundances of species in sites and where the species are characterized by traits and sites by environmental variables. The trait data and environment data form the external constraints and the question is which traits and environmental variables are associated, how these associations drive species abundances and how they can be displayed in biplots. With microbiome data becoming widely available, these and related multivariate methods deserve more study as they might be routinely used in the future.}, bibtype = {article}, author = {ter Braak, Cajo J.F. and Šmilauer, Petr and Dray, Stéphane}, doi = {10.1007/s10651-017-0395-x}, journal = {Environmental and Ecological Statistics} }
@article{ title = {Beyond neutrality: disentangling the effects of species sorting and spurious correlations in community analysis}, type = {article}, year = {2018}, keywords = {direct gradient analysis,environmental effect,limited dispersal,metacommunity ecology,moran spectral,neutral dynamics,randomization,spatial autocorrelation,spatially constrained null model,variation partitioning}, pages = {1737-1747}, volume = {99}, websites = {http://doi.org/10.1002/ecy.2376%0Ahttp://doi.wiley.com/10.1002/ecy.2376}, id = {0cadbf66-a953-3fbb-8fba-9cd7af0d79cf}, created = {2018-08-21T14:25:41.643Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2018-11-19T09:13:27.393Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Clappe2018}, private_publication = {false}, abstract = {The methods of direct gradient analysis and variation partitioning are the most widely used frameworks to evaluate the contributions of species sorting to metacommunity structure. In many cases, however, species are also driven by spatial processes that are independent of environmental heterogeneity (e.g., neutral dynamics). As such, spatial autocorrelation can occur independently in both species (due to limited dispersal) and the environmental data, leading to spurious correlations between species distributions and the spatialized (i.e., spatially-autocorrelated) environment. In these cases, the method of variation partitioning may present high Type I error rates (i.e., reject the null hypothesis more often than the pre-established critical level) and inflated estimates regarding the environmental component that is used to estimate the importance of species sorting. In this paper, we (1) demonstrate that metacommunities driven by neutral dynamics (via limited dispersal) alone or in combination with species sorting leads to inflated estimates and Type I error rates when testing for the importance of species sorting; and (2) propose a general and flexible new variation partitioning procedure to adjust for spurious contributions due to spatial autocorrelation from the environmental fraction. We used simulated metacommunity data driven by pure neutral, pure species sorting, and mixed (i.e. neutral + species sorting dynamics) processes to evaluate the performances of our new methodological framework. We also demonstrate the utility of the proposed framework with an empirical plant dataset in which we show that half of the variation initially due to the environment by the standard variation partitioning framework was due to spurious correlations.}, bibtype = {article}, author = {Clappe, Sylvie and Dray, Stéphane and Peres-Neto, Pedro R.}, doi = {10.1002/ecy.2376}, journal = {Ecology}, number = {8} }
@article{ title = {Supervised Multiblock Analysis in R with the ade4 Package}, type = {article}, year = {2018}, pages = {1-17}, volume = {86}, id = {5d92a843-15b8-33fa-a79f-231091a877dc}, created = {2018-09-06T11:29:17.268Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:49:10.860Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Bougeard2018}, private_publication = {false}, bibtype = {article}, author = {Bougeard, Stéphanie and Dray, Stéphane}, doi = {10.18637/jss.v086.i01}, journal = {Journal of Statistical Software}, number = {1} }
@article{ title = {Simple parametric tests for trait–environment association}, type = {article}, year = {2018}, keywords = {CWM of traits,community ecology,community-level test,environmental gradients,fourth-corner,functional traits,modified test,species niche centroid,species-level test,statistical ecology,trait–environment relationship}, pages = {801-811}, volume = {29}, id = {67d88eb1-4036-3208-8981-86a28b1b6242}, created = {2018-11-19T09:13:27.172Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:49:38.237Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {TerBraak2018a}, private_publication = {false}, abstract = {Question The community weighted means (CWM) approach is an easy way of analyzing trait-environment association by regressing (or correlating) the mean trait per plot against an environmental variable and assessing the statistical significance of the slope or the associated correlation coefficient. However, the CWM approach does not yield valid tests as random traits (or random indicator values) are far too often judged significantly related to the environmental variable, even when the trait and environmental variable are extrinsic to (not derived from) the community data. Existing solutions are the ZS-modified test (Zelený & Schaffers 2012) and the max (or sequential) test based on the fourth-corner correlation. Both tests are based on permutations which become cumbersome when many tests need to be carried out and many permutations are required as in methods that correct for multiple testing. The main goal of this paper is to compare these existing permutation-based solutions and to develop a quick and easy parametric test that can replace them. Methods This paper decomposes the fourth-corner correlation in two ways, which suggests a simple parametric approach consisting of assessing the significances of two linear regressions, one plot-level test as in the CWM approach and one species-level test, the reverse of the CWM approach, that regresses the environmental mean per species (i.e. the species niche centroid) on to the trait. The tests are combined by taking the maximum P-value. The type I error rates and power of this parametric max test is examined by simulation of one- and two-dimensional Gaussian models and log-linear models. Results The ZS-modified test and the fourth-corner max test are conservative in different scenarios, the ZS-modified test being even more conservative than fourth-corner. The new parametric max test is shown to control the type I error and has equal or even higher power than permutation tests based on fourth-corner, the ZS-modified test and variants thereof. A weighted version of the new test showed inflated type I error. Conclusion The combination of two simple regressions is a good alternative for the fourth-corner and the ZS-modified test. This combination is also applicable when multiple trait measurements are made per plot.}, bibtype = {article}, author = {ter Braak, Cajo J.F. and Peres-Neto, Pedro R. and Dray, Stéphane}, doi = {10.1111/jvs.12666}, journal = {Journal of Vegetation Science} }
@article{ title = {Optimizing the choice of a spatial weighting matrix in eigenvector-based methods}, type = {article}, year = {2018}, keywords = {Moran's eigenvector maps (MEM),community ecology,community simulation,connection scheme,inference of ecological processes from spatial pat,multiscale spatial patterns,optimization,principal coordinates of neighbor matrices (PCNM),spatial autocorrelation,spatial eigenvector mapping (SEVM),spatial weighting matrix,type I error rate inflation}, pages = {2159-2166}, volume = {99}, id = {0e6eeb9b-c61c-3d11-bee6-8ce92dc58db8}, created = {2018-11-19T09:13:27.174Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:49:26.001Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Bauman2018a}, private_publication = {false}, abstract = {Abstract Eigenvector-mapping methods such as Moran's eigenvector maps (MEM) are derived from a spatial weighting matrix (SWM) that describes the relations among a set of sampled sites. The specification of the SWM is a crucial step, but the SWM is generally chosen arbitrarily, regardless of the sampling design characteristics. Here, we compare the statistical performances of different types of SWMs (distance-based or graph-based) in contrasted realistic simulation scenarios. Then, we present an optimization method and evaluate its performances compared to the arbitrary choice of the most-widely used distance-based SWM. Results showed that the distance-based SWMs generally had lower power and accuracy than other specifications, and strongly underestimated spatial signals. The optimization method, using a correction procedure for multiple tests, had a correct type I error rate, and had higher power and accuracy than an arbitrary choice of the SWM. Nevertheless, the power decreased when too many SWMs were compared, resulting in a trade-off between the gain of accuracy and the loss of power. We advocate that future studies should optimize the choice of the SWM using a small set of appropriate candidates. R functions to implement the optimization are available in the adespatial package and are detailed in a tutorial.}, bibtype = {article}, author = {Bauman, David and Drouet, Thomas and Fortin, Marie Josée and Dray, Stéphane}, doi = {10.1002/ecy.2469}, journal = {Ecology}, number = {10} }
@book{ title = {Multivariate Analysis of Ecological Data with ade4}, type = {book}, year = {2018}, pages = {329}, websites = {http://link.springer.com/10.1007/978-1-4939-8850-1}, publisher = {Springer}, city = {New York}, id = {04f8fc2f-830a-3295-b2ff-9f78cfe43673}, created = {2018-11-21T12:46:21.996Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:53:12.667Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Thioulouse2018}, private_publication = {false}, abstract = {This book introduces the ade4 package for R which provides multivariate methods for the analysis of ecological data. It is implemented around the mathematical concept of the duality diagram, and provides a unified framework for multivariate analysis. The authors offer a detailed presentation of the theoretical framework of the duality diagram and also of its application to real-world ecological problems. These two goals may seem contradictory, as they concern two separate groups of scientists, namely statisticians and ecologists. However, statistical ecology has become a scientific discipline of its own, and the good use of multivariate data analysis methods by ecologists implies a fair knowledge of the mathematical properties of these methods. The organization of the book is based on ecological questions, but these questions correspond to particular classes of data analysis methods. The first chapters present both usual and multiway data analysis methods. Further chapters are dedicated for example to the analysis of spatial data, of phylogenetic structures, and of biodiversity patterns. One chapter deals with multivariate data analysis graphs. In each chapter, the basic mathematical definitions of the methods and the outputs of the R functions available in ade4 are detailed in two different boxes. The text of the book itself can be read independently from these boxes. Thus the book offers the opportunity to find information about the ecological situation from which a question raises alongside the mathematical properties of methods that can be applied to answer this question, as well as the details of software outputs. Each example and all the graphs in this book come with executable R code.}, bibtype = {book}, author = {Thioulouse, Jean and Dray, Stéphane and Dufour, Anne-Béatrice and Siberchicot, Aurélie and Jombart, Thibaut and Pavoine, Sandrine}, doi = {10.1007/978-1-4939-8850-1} }
@article{ title = {Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait-environment relationships}, type = {article}, year = {2018}, keywords = {Moran's spectral randomization,community ecology,fourth-corner analysis,functional ecology,null models,type I error}, pages = {2667-2674}, volume = {99}, websites = {http://doi.wiley.com/10.1002/ecy.2530}, id = {a07734c9-bb7e-390c-8c8b-f862321e3d85}, created = {2018-12-20T13:56:28.327Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-08-07T12:53:19.875Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Braga2018}, private_publication = {false}, abstract = {The fourth-corner analysis aims to quantify and test for relationships between species traits and site-specific environmental variables, mediated by site-specific species abundances. Since there is no common unit of observation, the significance of the relationships is tested using a double permutation procedure (site based and species based). This method implies that all species and sites are independent of each other. However, this fundamental hypothesis might be flawed because of phylogenetic relatedness between species and spatial autocorrelation in the environmental data. Here, using a simulation-based experiment, we demonstrate how the presence of spatial and phylogenetic autocorrelations can, in some circumstances, lead to inflated type I error rates, suggesting that signifi- cant associations can be misidentified. As an alternative, we propose a new randomization approach designed to avoid this issue, based on Moran’s spectral randomization. In this approach, standard permutations are replaced by constrained randomizations so that the distribution of the statistic under the null hypothesis is built with additional constraints to preserve the phylogenetic and spatial structures of the observed data. The inclusion of this new randomization approach provides total control over type I error rates and should be used in real studies where spatial and phylogenetic autocorrelations often occur.}, bibtype = {article}, author = {Braga, João and ter Braak, Cajo J. F. and Thuiller, Wilfried and Dray, Stéphane}, doi = {10.1002/ecy.2530}, journal = {Ecology}, number = {12} }
@article{ title = {A critical issue in model-based inference for studying trait-based community assembly and a solution}, type = {article}, year = {2017}, pages = {e2885}, volume = {5}, id = {f13ee790-86c8-390e-927f-b24395f24c42}, created = {2017-01-31T15:46:39.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-12-20T14:24:26.358Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {TerBraak2017}, private_publication = {false}, abstract = {Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one site-based and the other species-based and by assessing significance by the largest of the two p-values (the pmax test). Recently, regression-based methods using generalized linear models (GLM) have been proposed as a promising alternative with statistical inference via site-based resampling. We investigated the performance of this new approach along with approaches that mimicked the pmax test using GLM instead of fourth-corner. By simulation using models with additional random variation in the species response to the environment, the site-based resampling tests using GLM are shown to have severely inflated type I error, of up to 90%, when the nominal level is set as 5%. In addition, predictive modelling of such data using site-based cross-validation very often identified trait-environment interactions that had no predictive value. The problem that we identify is not an “omitted variable bias” problem as it occurs even when the additional random variation is independent of the observed trait and environment data. Instead, it is a problem of ignoring a random effect. In the same simulations, the GLM-based pmax test controlled the type I error in all models proposed so far in this context, but still gave slightly inflated error in more complex models that included both missing (but important) traits and missing (but important) environmental variables. For screening the importance of single trait-environment combinations, the fourth-corner test is shown to give almost the same results as the GLM-based tests in far less computing time.}, bibtype = {article}, author = {ter Braak, Cajo and Dray, Stéphane and Peres-Neto, Pedro}, doi = {10.7717/peerj.2885}, journal = {PeerJ} }
@article{ title = {Linking trait variation to the environment: Critical issues with community-weighted mean correlation resolved by the fourth-corner approach}, type = {article}, year = {2017}, pages = {806-816}, volume = {40}, id = {fb2e073b-9436-39c4-9357-1dcee533715f}, created = {2017-06-27T12:55:04.218Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-08-23T21:03:59.630Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Peres-Neto2017}, private_publication = {false}, abstract = {Establishing trait-environment relationships has become routine in community ecology. Here, we demonstrate that the Community Weighted Means correlation (CWM) and its parallel approach in linking trait variation to the environment, the Species Niche Centroid correlation (SNC), have important shortcomings, arguing against their continuing application. Using mathematical derivations and simulations, we show that the two major issues are inconsistent parameter estimation and unacceptable significance rates when only the environment or only traits are structuring species distributions, but they themselves are not linked. We show how both CWM and SNC are related to the fourth-corner correlation and propose to replace all by the Chessel fourth-corner correlation, which is the fourth-corner correlation divided by its maximum attainable value. We propose an appropriate hypothesis testing procedure that is not only unbiased but also has much greater statistical power in detecting trait-environmental relationships. We derive an additive framework in which trait variation is partitioned among and within communities, which can be then modeled against the environment. We finish by presenting a contrast between methods and an application of our proposed framework across 85 lake-fish metacommunities.This article is protected by copyright. All rights reserved.}, bibtype = {article}, author = {Peres-Neto, Pedro R. and Dray, Stéphane and ter Braak, Cajo J.F.}, doi = {10.1111/ecog.02302}, journal = {Ecography} }
@article{ title = {Factors shaping community assemblages and species occurrence of different trophic levels}, type = {article}, year = {2017}, pages = {4745–4754}, volume = {7}, id = {27b66af1-127b-3daf-9f07-7bceeab5ece4}, created = {2017-08-07T11:59:50.555Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-06-26T07:52:32.551Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Trivellone2017}, private_publication = {false}, abstract = {Species assemblages are the results of various processes, including dispersion and habitat filtering. Disentangling the effects of these different processes is challenging for statistical analysis, especially when biotic interactions should be considered. In this study, we used plants (producers) and leafhoppers (phytophagous) as model organisms, and we investigated the relative importance of abiotic versus biotic factors that shape community assemblages, and we infer on their biotic interactions by applying three-step statistical analysis. We applied a novel statistical analysis, that is, multiblock Redundancy Analysis (mbRA, step 1) and showed that 51.8% and 54.1% of the overall variation in plant and leafhopper assemblages are, respectively, explained by the two multiblock models. The most important blocks of variables to explain the variations in plant and leafhopper assemblages were local topography and biotic factors. Variation partitioning analysis (step 2) showed that pure abiotic filtering and pure biotic processes were relatively less important than their combinations, suggesting that biotic relationships are strongly structured by abiotic conditions. Pairwise co-occurrence analysis (step 3) on generalist leafhoppers and the most common plants identified 40 segregated species pairs (mainly between plant species) and 16 aggregated pairs (mainly between leafhopper species). Pairwise analysis on specialist leafhoppers and potential host plants clearly revealed aggregated patterns. Plant segregation suggests heterogeneous resource availability and competitive interactions, while leafhopper aggregation suggests host feeding differentiation at the local level, different feeding microhabitats on host plants, and similar environmental requirements of the species. Using the novel mbRA, we disentangle for the first time the relative importance of more than five distinct groups of variables shaping local species communities. We highlighted the important role of abiotic processes mediated by bottom-up effects of plants on leafhopper communities. Our results revealed that in-field structure diversification and trophic interactions are the main factors causing the co-occurrence patterns observed.}, bibtype = {article}, author = {Trivellone, Valeria and Bougeard, Stephanie and Giavi, Simone and Krebs, Patrik and Balseiro, Diego and Dray, Stéphane and Moretti, Marco}, doi = {10.1002/ece3.3061}, journal = {Ecology and Evolution} }
@inproceedings{ title = {Environment, traits, space and phylogeny: integrating constraints in the analysis of ecological data tables}, type = {inproceedings}, year = {2017}, websites = {http://www.lirmm.fr/mceb2017/}, city = {Porquerolles, France}, id = {26d80d9f-3814-3e3f-a61c-f22d3ec109a8}, created = {2017-08-24T12:30:15.556Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-08-24T12:30:15.556Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2017}, source_type = {inproceedings}, notes = {Invited conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Mathematical and Computational Evolutionary Biology Conference} }
@inproceedings{ title = {Analyse spatiale multi-échelles de données écologiques avec adespatial}, type = {inproceedings}, year = {2017}, city = {Anglet, France}, id = {e8ed6469-1f40-343f-b791-b96eda2b66e4}, created = {2017-08-24T12:30:15.581Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-08-24T12:30:15.581Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2017a}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {6èmes Rencontres R} }
@article{ title = {adegraphics: an S4 lattice-based package for the representation of multivariate data}, type = {article}, year = {2017}, pages = {198-2012}, volume = {9}, websites = {https://journal.r-project.org/archive/2017/RJ-2017-042/RJ-2017-042.pdf}, id = {67c3d2d5-5d94-3625-be9d-a9b6b1165edb}, created = {2018-02-19T09:43:32.697Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2018-02-19T09:43:34.289Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Siberchicot2017}, private_publication = {false}, abstract = {The ade4 package provides tools for multivariate analyses. Whereas new statistical methods have been added regularly in the package since its first release in 2002, the graphical functions, that are used to display the main outputs of an analysis, have not benefited from such enhancements. In this context, the adegraphics package, available on CRAN since 2015, is a complete reimplementation of the ade4 graphical functionalities but with large improvements. The package uses the S4 object system (each graph is an object) and is based on the graphical framework provided by lattice and grid. We give a brief description of the package and illustrate some important functionalities to build elegant graphs.}, bibtype = {article}, author = {Siberchicot, Aurélie and Julien-Laferrière, Alice and Dufour, Anne-Béatrice and Thioulouse, Jean and Dray, Stéphane}, journal = {The R Journal}, number = {2} }
@inproceedings{ title = {Couplage des données de biodiversité : prise en compte de l’originalité des structures de données}, type = {inproceedings}, year = {2017}, city = {Paris, France}, id = {78cb60c3-7c8e-380b-b807-62dda1f0a734}, created = {2020-01-29T13:05:12.631Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-01-29T13:05:12.631Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Ecoscope, Fondation pour la Recherche sur la Biodiversité, 12 December} }
@article{ title = {Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification}, type = {article}, year = {2016}, pages = {492-517}, volume = {94}, websites = {http://linkinghub.elsevier.com/retrieve/pii/S1055790315003218}, id = {d86dcb49-2da8-3007-896a-ea6c89d63f91}, created = {2015-12-03T13:09:12.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2016}, private_publication = {false}, abstract = {The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria.}, bibtype = {article}, author = {Covain, Raphaël and Fisch-Muller, Sonia and Oliveira, Claudio and Mol, Jan H. and Montoya-Burgos, Juan I. and Dray, Stéphane}, doi = {10.1016/j.ympev.2015.10.018}, journal = {Molecular Phylogenetics and Evolution} }
@article{ title = {The global spectrum of plant form and function}, type = {article}, year = {2016}, pages = {167-171}, volume = {529}, websites = {http://dx.doi.org/10.1038/nature16489,http://www.nature.com/doifinder/10.1038/nature16489}, month = {12}, publisher = {Nature Publishing Group}, day = {23}, id = {526955c0-508e-319e-8f49-6f7e7ce42bfc}, created = {2015-12-26T23:15:53.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.356Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Diaz2016}, private_publication = {false}, abstract = {Earth is home to a remarkable diversity of plant forms and life histories, yet comparatively few essential trait combinations have proved evolutionarily viable in today’s terrestrial biosphere. By analysing worldwide variation in six major traits critical to growth, survival and reproduction within the largest sample of vascular plant species ever compiled, we found that occupancy of six-dimensional trait space is strongly concentrated, indicating coordination and trade-offs. Three- quarters of trait variation is captured in a two-dimensional global spectrum of plant form and function. One major dimension within this plane reflects the size of whole plants and their parts; the other represents the leaf economics spectrum, which balances leaf construction costs against growth potential. The global plant trait spectrum provides a backdrop for elucidating constraints on evolution, for functionally qualifying species and ecosystems, and for improving models that predict future vegetation based on continuous variation in plant form and function.}, bibtype = {article}, author = {Díaz, Sandra and Kattge, Jens and Cornelissen, Johannes H C and Wright, Ian J. and Lavorel, Sandra and Dray, Stéphane and Reu, Björn and Kleyer, Michael and Wirth, Christian and Prentice, I. Colin and Garnier, Eric and Bönisch, Gerhard and Westoby, Mark and Poorter, Hendrik and Reich, Peter B and Moles, Angela T and Dickie, John and Gillison, Andrew N and Zanne, Amy E and Chave, Jérôme and Wright, S. Joseph and Sheremet’ev, Serge N. and Jactel, Hervé and Baraloto, Christopher and Cerabolini, Bruno and Pierce, Simon and Shipley, Bill and Kirkup, Donald and Casanoves, Fernando and Joswig, Julia S and Günther, Angela and Falczuk, Valeria and Rüger, Nadja and Mahecha, Miguel D. and Gorné, Lucas D.}, doi = {10.1038/nature16489}, journal = {Nature} }
@article{ title = {Addressing ecological effects of radiation on populations and ecosystems to improve protection of the environment against radiation: Agreed statements from a Consensus Symposium.}, type = {article}, year = {2016}, keywords = {Consensus development,Ecological risk assessment,Ecosystems,Environmental protection,Populations,Radiation effects}, pages = {21-29}, volume = {158-159}, websites = {http://www.sciencedirect.com/science/article/pii/S0265931X16300832}, month = {4}, day = {5}, id = {eb610f24-bd7d-3f47-a752-42df408f24da}, created = {2016-04-22T13:35:18.000Z}, accessed = {2016-04-20}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Brechignac2016}, private_publication = {false}, abstract = {This paper reports the output of a consensus symposium organized by the International Union of Radioecology in November 2015. The symposium gathered an academically diverse group of 30 scientists to consider the still debated ecological impact of radiation on populations and ecosystems. Stimulated by the Chernobyl and Fukushima disasters' accidental contamination of the environment, there is increasing interest in developing environmental radiation protection frameworks. Scientific research conducted in a variety of laboratory and field settings has improved our knowledge of the effects of ionizing radiation on the environment. However, the results from such studies sometimes appear contradictory and there is disagreement about the implications for risk assessment. The Symposium discussions therefore focused on issues that might lead to different interpretations of the results, such as laboratory versus field approaches, organism versus population and ecosystemic inference strategies, dose estimation approaches and their significance under chronic exposure conditions. The participating scientists, from across the spectrum of disciplines and research areas, extending also beyond the traditional radioecology community, successfully developed a constructive spirit directed at understanding discrepancies. From the discussions, the group has derived seven consensus statements related to environmental protection against radiation, which are supplemented with some recommendations. Each of these statements is contextualized and discussed in view of contributing to the orientation and integration of future research, the results of which should yield better consensus on the ecological impact of radiation and consolidate suitable approaches for efficient radiological protection of the environment.}, bibtype = {article}, author = {Bréchignac, François and Oughton, Deborah and Mays, Claire and Barnthouse, Lawrence and Beasley, James C and Bonisoli-Alquati, Andrea and Bradshaw, Clare and Brown, Justin and Dray, Stéphane and Geras'kin, Stanislav and Glenn, Travis and Higley, Kathy and Ishida, Ken and Kapustka, Lawrence and Kautsky, Ulrik and Kuhne, Wendy and Lynch, Michael and Mappes, Tapio and Mihok, Steve and Møller, Anders P and Mothersill, Carmel and Mousseau, Timothy A and Otaki, Joji and Pryakhin, Evgeny and Rhodes, Olin E and Salbu, Brit and Strand, Per and Tsukada, Hirofumi}, doi = {10.1016/j.jenvrad.2016.03.021}, journal = {Journal of Environmental Radioactivity} }
@article{ title = {Spatial distribution of a large herbivore community at waterholes: An assessment of its stability over years in Hwange National Park, Zimbabwe}, type = {article}, year = {2016}, pages = {e0153639}, volume = {11}, id = {f27b3aa6-28b6-3697-9b9a-9650df8f0d3e}, created = {2016-06-17T08:51:45.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-08-24T14:55:34.589Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Chamaille-Jammes2016}, private_publication = {false}, abstract = {The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes.}, bibtype = {article}, author = {Chamaillé-Jammes, Simon and Charbonnel, Anaïs and Dray, Stéphane and Madzikanda, Hillary and Fritz, Hervé}, doi = {10.1371/journal.pone.0153639}, journal = {PLoS ONE}, number = {4} }
@phdthesis{ title = {Environnement, traits, espace et phylogénie : intégrer des contraintes dans l’analyse d’un tableau écologique}, type = {phdthesis}, year = {2016}, pages = {80}, institution = {Université Lyon I}, id = {fb722068-0eb9-3838-8ef0-c10eacda4b4a}, created = {2016-06-17T14:57:44.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.842Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2016}, user_context = {Habilitation à Diriger des Recherches}, private_publication = {false}, bibtype = {phdthesis}, author = {Dray, Stéphane} }
@article{ title = {Interspecific interference competition at the resource patch scale: do large herbivores spatially avoid elephants while accessing water?}, type = {article}, year = {2016}, pages = {1574-1585}, volume = {85}, id = {060dc372-f214-3f79-838d-443a7051d428}, created = {2016-11-20T08:40:20.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Ferry2016}, private_publication = {false}, abstract = {Animals may anticipate and try to avoid, at some costs, physical encounters with other competitors. This may ultimately impact their foraging distribution and intake rates. Such cryptic interference competition is difficult to measure in the field, and extremely little is known at the interspecific level. We tested the hypothesis that smaller species avoid larger ones because of potential costs of interference competition and hence expected them to segregate from larger competitors at the scale of a resource patch. We assessed fine-scale spatial segregation patterns between three African herbivore species (zebra Equus quagga, kudu Tragelaphus strepsiceros and giraffe Giraffa camelopardalis) and a megaherbivore, the African elephant Loxodonta africana, at the scale of water resource patches in the semi-arid ecosystem of Hwange National Park, Zimbabwe. Nine waterholes were monitored every two weeks during the dry season of a drought year, and observational scans of the spatial distribution of all herbivores were performed every 15 min. We developed a methodological approach to analyse such fine-scale spatial data. Elephants increasingly used waterholes as the dry season progressed, as did the probability of co-occurrence and agonistic interaction with elephants for the three study species. All three species segregated from elephants at the beginning of the dry season, suggesting a spatial avoidance of elephants and the existence of costs of being close to them. However, contrarily to our expectations, herbivores did not segregate from elephants the rest of the dry season but tended to increasingly aggregate with elephants as the dry season progressed. We discuss these surprising results and the existence of a trade-off between avoidance of interspecific interference competition and other potential factors such as access to quality water, which may have relative associated costs that change with the time of the year.}, bibtype = {article}, author = {Ferry, Nicolas and Dray, Stéphane and Fritz, Hervé and Valeix, Marion}, doi = {10.1111/1365-2656.12582}, journal = {Journal of Animal Ecology} }
@article{ title = {Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)}, type = {article}, year = {2015}, pages = {242-249}, volume = {15}, id = {e30828e7-dce0-3860-ac1d-1362d15ad6f2}, created = {2015-01-28T12:25:33.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2015}, private_publication = {false}, abstract = {The use of next-generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differ- ences and (or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene data sets.}, bibtype = {article}, author = {Dray, Stéphane and Pavoine, Sandrine and Aguirre de Carcer, Daniel}, doi = {10.1111/1755-0998.12300}, journal = {Molecular Ecology Resources} }
@article{ title = {Principal component analysis with missing values: a comparative survey of methods}, type = {article}, year = {2015}, pages = {657-667}, volume = {216}, id = {56023fe4-1664-39aa-a69e-384c2cc3f87f}, created = {2015-01-28T12:25:33.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2015a}, private_publication = {false}, abstract = {Principal component analysis (PCA) is a standard technique to summarize the main structures of a data table containing the measurements of several quantitative variables for a number of individuals. Here, we study the case where some of the data values are missing and propose a review of methods which accommodate PCA to missing data. In plant ecology, this statistical challenge relates to the current effort to compile global plant functional trait databases producing matrices with a large amount of missing values. We present several techniques to consider or estimate (impute) missing values in PCA and compare them using theoretical considerations. We carried out a simulation study to evaluate the relative merits of the different approaches in various situations (correlation structure, number of variables and individuals, and percentage of missing values) and also applied them on a real data set. Lastly, we discuss the advantages and drawbacks of these approaches, the potential pitfalls and future challenges that need to be addressed in the future.}, bibtype = {article}, author = {Dray, Stéphane and Josse, Julie}, doi = {10.1007/s11258-014-0406-z}, journal = {Plant Ecology} }
@inproceedings{ title = {An integrated web server and R package for data sharing and reproducible research in ecology}, type = {inproceedings}, year = {2015}, city = {Lyon, France}, id = {3436e16c-91e3-3807-9941-cd6438ca94c0}, created = {2015-01-28T14:41:28.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2015b}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {RLyon, 15 January} }
@article{ title = {Generating spatially constrained null models for irregularly spaced data using Moran spectral randomization methods}, type = {article}, year = {2015}, pages = {1169-1178}, volume = {6}, websites = {http://doi.wiley.com/10.1111/2041-210X.12407}, id = {a279f023-a730-316b-909e-e8b320088550}, created = {2015-10-14T11:05:34.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2018-11-21T16:14:00.134Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Wagner2015}, private_publication = {false}, abstract = {Spatial autocorrelation jeopardizes the validity of statistical inference, for example correlation and regression analysis. Restricted randomization methods can account for the effect of spatial autocorrelation in the observed data by building it into an empirical null model for hypothesis testing. This can be achieved, for example, based on conditional simulation, which fits a highly parameterized geostatistical model to the observed spatial structure, or, for data observed on a regular transect or grid, with Fourier spectral randomization methods that can flexibly model spatial structure at any scale. This study uses Moran eigenvector maps to extend spectral randomization to irregularly spaced samples. We present different algorithms to perform restricted randomization to suit different types of research questions: individual randomization of each variable, joint randomization of a group of variables while keeping within-group correlations fixed, and randomization with a fixed correlation between original data and randomized replicates (e.g. as input for simulation studies). The performance of the proposed Moran spectral randomization methods for regularly and irregularly spaced samples is assessed with correlation analysis of simulated data. Moran spectral randomization closely matched the spatial structure of original simulated data sets, with identical or nearly identical Moran's I values and power spectra, depending on the algorithm. In correlation analysis of two spatially autocorrelated variables, Moran spectral randomization produced correct type I error rates for stationary spatial data, even for very small and highly irregular samples, but was sensitive to linear trend. When one or both variables lacked spatial structure, Moran spectral randomization tests were more conservative than correlation t-tests. The proposed Moran spectral randomization method requires a minimum of parameterization and is able to address multivariate data with spatial structure at multiple scales, with the option of controlling levels of correlation with the original data. It can provide technically unlimited numbers of randomizations even for small samples while closely maintaining the spatial characteristics of uni- or multivariate data at all spatial scales. The method is applicable for correlation analysis of stationary, autocorrelated spatial or temporal series. Further research should assess whether the method can be extended to multiple regression analysis.}, bibtype = {article}, author = {Wagner, Helene H. and Dray, Stéphane}, doi = {10.1111/2041-210X.12407}, journal = {Methods in Ecology and Evolution}, number = {10} }
@inproceedings{ title = {The adephylo package}, type = {inproceedings}, year = {2015}, city = {Lausanne, Suisse}, id = {d8e33ded-4f50-3f1a-a2d7-5b2aacfdf3a8}, created = {2019-03-08T09:38:40.504Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-08T09:38:40.504Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2015c}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Theories and Methods in Spatial Community Modelling, 21-24 April} }
@article{ title = {Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation}, type = {article}, year = {2014}, keywords = {alps,fourth-corner matrix,functional ecology,permutation procedures,rlq tables,trait-environment relationship}, pages = {14-21}, volume = {95}, websites = {http://www.esajournals.org/doi/abs/10.1890/13-0196.1}, id = {ef9b5c32-c2cc-3c77-85e5-7c2ebb0a5d90}, created = {2014-01-21T14:27:43.000Z}, accessed = {2014-01-21}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.661Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2014}, private_publication = {false}, abstract = {Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L (species distribution across samples), R (environmental characteristics of samples), and Q (species traits). Among the available methods, the so-called fourth-corner and RLQ methods are two appealing alternatives that provide a direct way to test and estimate trait–environment relationships. Both methods are based on the analysis of the fourth-corner matrix, which crosses traits and environmental variables weighted by species abundances. However, they differ greatly in their outputs: RLQ is a multivariate technique that provides ordination scores to summarize the joint structure among the three tables, whereas the fourth-corner method mainly tests for individual trait–environment relationships (i.e., one trait and one environmental variable at a time). Here, we illustrate how the complementarity between these two methods can be exploited to promote new ecological knowledge and to improve the study of trait–environment relationships. After a short description of each method, we apply them to real ecological data to present their different outputs and provide hints about the gain resulting from their combined use.}, bibtype = {article}, author = {Dray, Stéphane and Choler, P and Dolédec, Sylvain and Peres-Neto, P R and Thuiller, Wilfried and Pavoine, Sandrine and ter Braak, Cajo J.F.}, journal = {Ecology}, number = {1} }
@article{ title = {Functional analysis of Normalized Difference Vegetation Index curves reveals overwinter mule deer survival is driven by both spring and autumn phenology}, type = {article}, year = {2014}, pages = {20130196}, volume = {369}, id = {e865a50d-47f5-3bfa-b1ac-630352138ab3}, created = {2014-04-14T14:08:28.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Hurley2014}, private_publication = {false}, abstract = {Large herbivore populations respond strongly to remotely sensed measures of primary productivity. Whereas most studies in seasonal environments have focused on the effects of spring plant phenology on juvenile survival, recent studies demonstrated that autumn nutrition also plays a crucial role. We tested for both direct and indirect (through body mass) effects of spring and autumn phenology on winter survival of 2315 mule deer fawns across a wide range of environmental conditions in Idaho, USA. We first performed a functional analysis that identified spring and autumn as the key periods for structuring the among-population and among-year variation of primary production (approximated from 1 km Advanced Very High Resolution Radiometer Normalized Difference Vegetation Index (NDVI)) along the growing season. A path analysis showed that early winter precipitation and direct and indirect effects of spring and autumn NDVI functional components accounted for 45% of observed variation in overwinter survival. The effect size of autumn phenology on body mass was about twice that of spring phenology, while direct effects of phenology on survival were similar between spring and autumn. We demonstrate that the effects of plant phenology vary across ecosystems, and that in semi-arid systems, autumn may be more important than spring for overwinter survival.}, bibtype = {article}, author = {Hurley, Mark A and Hebblewhite, Mark and Gaillard, Jean-Michel and Dray, Stéphane and Taylor, Kyle A and Smith, W. K. and Zager, Pete and Bonenfant, Christophe}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences} }
@inbook{ type = {inbook}, year = {2014}, pages = {289-300}, publisher = {CRC Press}, id = {db5cb599-64b8-3601-a5fb-990a7382c5d8}, created = {2014-05-15T11:04:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2014a}, private_publication = {false}, bibtype = {inbook}, author = {Dray, Stéphane}, editor = {Blasius, J and Greenacre, M}, chapter = {Analysing a pair of tables: coinertia analysis and duality diagrams}, title = {Visualization and verbalization of data} }
@article{ title = {Spatially constrained clustering of ecological networks}, type = {article}, year = {2014}, pages = {771-779}, volume = {5}, websites = {http://doi.wiley.com/10.1111/2041-210X.12208}, day = {20}, id = {70044472-ded5-3765-bd4e-3e06dbd32cbe}, created = {2014-08-22T15:10:01.000Z}, accessed = {2014-08-17}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Miele2014}, private_publication = {false}, abstract = {Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g. populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar biological entities are firstly identified and the spatial information is used afterwards to improve the ecological interpretation. We develop an integrative approach to retrieve groups of nodes that are geographically close and ecologically similar. Our model-based spatially constrained method embeds the geographical information within a regularization framework by adding some constraints to the maximum likelihood estimation of parameters. A simulation study and the analysis of two real data sets demonstrate that our approach is able to detect complex spatial patterns that are ecologically meaningful. The model-based framework allows us to consider external information (e.g. geographical proximities, covariates) in the analysis of ecological networks and appears to be an appealing alternative to consider such data.}, bibtype = {article}, author = {Miele, Vincent and Picard, Franck and Dray, Stéphane}, editor = {Peres-Neto, Pedro}, doi = {10.1111/2041-210X.12208}, journal = {Methods in Ecology and Evolution}, number = {8} }
@article{ title = {Statistical ecology comes of age}, type = {article}, year = {2014}, pages = {3-6}, volume = {10}, websites = {http://www.ncbi.nlm.nih.gov/pubmed/25540151}, month = {12}, id = {47890681-262f-3915-a795-469f045aa4d9}, created = {2015-01-05T16:33:03.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Gimenez2014}, private_publication = {false}, abstract = {The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1-4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.}, bibtype = {article}, author = {Gimenez, Olivier and Buckland, Stephen T and Morgan, Byron J T and Bez, Nicolas and Bertrand, Sophie and Choquet, Rémi and Dray, Stéphane and Etienne, Marie-Pierre and Fewster, Rachel and Gosselin, Frédéric and Mérigot, Bastien and Monestiez, Pascal and Morales, Juan M and Mortier, Frédéric and Munoz, François and Ovaskainen, Otso and Pavoine, Sandrine and Pradel, Roger and Schurr, Frank M and Thomas, Len and Thuiller, Wilfried and Trenkel, Verena and de Valpine, Perry and Rexstad, Eric}, doi = {10.1098/rsbl.2014.0698}, journal = {Biology Letters}, number = {12} }
@inproceedings{ title = {An integrated web server and R package for data sharing and reproducible research in ecology}, type = {inproceedings}, year = {2014}, city = {Lyon, France}, id = {7ec70b7c-403d-3bb7-affb-bccf9c051560}, created = {2015-01-28T14:41:28.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2014b}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Séminaire interne de l'UMR 5558, 28 October} }
@article{ title = {Reciprocal modulation of internal and external factors determines individual movements.}, type = {article}, year = {2013}, keywords = {Ursus arctos,animal movements,movement ecology,spatial ecology,spatial scales}, pages = {290-300}, volume = {82}, websites = {http://www.ncbi.nlm.nih.gov/pubmed/23039315}, day = {5}, id = {f9166b35-68ab-3fba-bf8f-919e02cfb46d}, created = {2012-08-27T08:25:49.000Z}, accessed = {2013-02-28}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Martin2013}, private_publication = {false}, abstract = {Movement is fundamental to individual and population dynamics, as it allows individuals to meet their basic requirements. Although movement patterns reflect interactions between internal and external factors, only few studies have examined the effects of these factors on movement simultaneously, and they generally focused on particular biological contexts (e.g. dispersal, foraging). However, the relative importance of these factors in driving individual routine movements might reflect a species' potential flexibility to cope with landscape changes and therefore buffer their potential impact on fitness. We used data from GPS collars on Scandinavian brown bears to investigate the relative role of these factors, as well as an additional factor (period of the year) on routine movements at two spatial scales (hourly and daily relocations). As expected, internal factors played a major role in driving movement, compared to external factors at both scales, but its relative importance was greater at a finer scale. In particular, the interaction between reproductive status and period of the year was one of the most influential variables, females being constrained by the movement capacity of their cubs in the first periods of the year. The effect of human disturbance on movement was also greater for females with cubs than for lone females. This study showed how reciprocal modulation of internal and external factors is shaping space use of brown bears. We stress that these factors should be studied simultaneously to avoid the risk of obtaining context-dependent inferences. Moreover, the study of their relative contribution is also highly relevant in the context of multiple-use landscapes, as human activities generally affect the landscape more than they affect the internal states of an individual. Species or individuals with important internal constraints should be less responsive to changes in their environment as they have less freedom from internal constraints and should thus be more sensitive to human alteration of the landscape, as shown for females with cubs in this study.}, bibtype = {article}, author = {Martin, Jodie and van Moorter, Bram and Revilla, Eloy and Blanchard, Pierrick and Dray, Stéphane and Quenette, Pierre-Yves and Allainé, Dominique and Swenson, Jon E}, doi = {10.1111/j.1365-2656.2012.02038.x}, journal = {Journal of Animal Ecology} }
@article{ title = {Does local habitat fragmentation affect large-scale distributions? The case of a specialist grassland bird}, type = {article}, year = {2013}, pages = {423-432}, volume = {19}, websites = {http://doi.wiley.com/10.1111/ddi.12019}, day = {9}, id = {fd78e892-3f34-3438-a5a4-29e10ccdedfe}, created = {2013-03-04T23:05:51.000Z}, accessed = {2013-03-04}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Reino2013}, private_publication = {false}, abstract = {Aim: Although the negative effects of habitat fragmentation have been widely documented at the landscape scale, much less is known about its impacts on species distributions at the biogeographical scale. We hypothesize that fragmentation influences the large-scale distribution of area- and edge-sensitive species by limiting their occurrence in regions with fragmented habitats, despite otherwise favourable environmental conditions. We test this hypothesis by assessing the interplay of climate and landscape factors influencing the distribution of the calandra lark, a grassland specialist that is highly sensitive to habitat fragmentation. Location: Iberia Peninsula, Europe. Methods: Ecological niche modelling was used to investigate the relative influence of climate/topography, landscape fragmentation and spatial structure on calandra lark distribution. Modelling assumed explicitly a hierarchically structured effect among explanatory variables, with climate/topography operating at broader spatial scales than landscape variables. An eigenvector-based spatial filtering approach was used to cancel bias introduced by spatial autocorrelation. The information theoretic approach was used in model selection, and variation partitioning was used to isolate the unique and shared effects of sets of explanatory variables. Results: Climate and topography were the most influential variables shaping the distribution of calandra lark, but incorporating landscape metrics contributed significantly to model improvement. The probability of calandra lark occurrence increased with total habitat area and declined with the number of patches and edge density. Variation partitioning showed a strong overlap between variation explained by climate/topography and landscape variables. After accounting for spatial structure in species distribution, the explanatory power of environmental variables remained largely unchanged. Main conclusions: We have shown here that landscape fragmentation can influence species distributions at the biogeographical scale. Incorporating fragmentation metrics into large-scale ecological niche models may contribute for a better understanding of mechanism driving species distributions and for improving predictive modelling of range shifts associated with land use and climate changes.}, bibtype = {article}, author = {Reino, Luís and Beja, Pedro and Araújo, Miguel B. and Dray, Stéphane and Segurado, Pedro}, editor = {Heikkinen, Dr. Risto}, doi = {10.1111/ddi.12019}, journal = {Diversity and Distributions} }
@article{ title = {A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients}, type = {article}, year = {2013}, keywords = {co-existence,environmental filtering,functional divergence,functional evenness,functional richness,functional trait,limiting}, pages = {794-806}, volume = {24}, websites = {http://doi.wiley.com/10.1111/jvs.12013}, day = {20}, id = {e1eade87-87b0-3239-b7ab-0a2bbc7ed1d7}, created = {2013-03-04T23:07:22.000Z}, accessed = {2013-03-04}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Mason2013}, private_publication = {false}, abstract = {Question: Which functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress gradients? Is their power affected by stochastic processes and variations in species richness along stress gradients? Methods: We used a simple community assembly model to explore the power of functional diversity indices across a wide range of ecological contexts. The model assumes that with declining stress the influence of niche complementarity on species fitness increases while that of environmental filtering decreases. We separately incorporated two trait-independent stochastic processes – mass and priority effects – in simulating species occurrences and abundances along a hypothetical stress gradient. We ran simulations where species richness was constant along the gradient, or increased, decreased or varied randomly with declining stress. We compared observed values for two indices of functional richness – total functional dendrogram length (FD) and convex hull volume (FRic) – with a matrix-swap null model (yielding indices SESFD and SESFRic) to remove any trivial effects of species richness. We also compared two indices that measure both functional richness and functional divergence – Rao quadratic entropy (Rao) and functional dispersion (FDis) – with a null model that randomizes abundances across species but within communities. This converts them to pure measures of functional divergence (SESRao and SESFDis). Results:When mass effects operated, only SESRao and SESFDis gave reasonable power, irrespective of how species richness varied along the stress gradient. FD, FRic, Rao and FDis had low power when species richness was constant, and variation in species richness greatly influenced their power. SESFRic and SESFD were unaffected by variation in species richness. When priority effects operated, FRic, SESFRic, Rao and FDis had good power and were unaffected by variation in species richness. Variation in species richness greatly affected FD and SESFD. SESRao and SESFDis had low power in the priority effects model but were unaffected by variation in species richness. Conclusions: Our results demonstrate that a reliable test for changes in assembly processes along stress gradients requires functional diversity indices measuring either functional richness or functional divergence. We recommend using SESFRic as a measure of functional richness and either SESRao or SESFDis (which are very closely related mathematically) as a measure of functional divergence. Used together, these indices of functional richness and functional divergence provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.}, bibtype = {article}, author = {Mason, Norman W.H. and de Bello, Francesco and Mouillot, David and Pavoine, Sandrine and Dray, Stéphane}, editor = {Zobel, Martin}, doi = {10.1111/jvs.12013}, journal = {Journal of Vegetation Science} }
@inproceedings{ title = {De la biologie à l'algèbre linéaire ... en passant par R. Expérimenter la notion de projection}, type = {inproceedings}, year = {2013}, city = {Lyon, France}, id = {88f1ab7f-a555-39d0-a327-b5c4ee6cb6e5}, created = {2013-09-02T07:32:26.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dufour2013}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dufour, Anne-Béatrice and Dray, Stéphane and Lobry, Jean and Thioulouse, Jean}, booktitle = {2èmes Rencontres R} }
@inproceedings{ title = {Méthodes de couplage de deux K-tableaux et collections de graphiques}, type = {inproceedings}, year = {2013}, city = {Lyon, France}, id = {1d2506b8-321d-3f6e-b3bf-926a4f04269d}, created = {2013-09-02T07:35:38.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Thioulouse2013}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Thioulouse, Jean and Siberchicot, Aurélie and Julien-Laferrière, Alice and Dufour, Anne-Béatrice and Dray, Stéphane}, booktitle = {2èmes Rencontres R} }
@inproceedings{ title = {Un site web d'enseignement R automatisé et à gestion partagée}, type = {inproceedings}, year = {2013}, city = {Lyon, France}, id = {d3abd221-56c4-3e02-beca-5f86d7c01f7c}, created = {2013-09-02T07:39:57.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Penel2013}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Penel, Simon and Dray, Stéphane and Dufour, Anne-Béatrice and Lobry, Jean and Mousset, Sylvain}, booktitle = {2èmes Rencontres R} }
@inproceedings{ title = {adegraphics : un package pour la représentation et l'analyse de données multivariées}, type = {inproceedings}, year = {2013}, city = {Lyon, France}, id = {85d06603-f3b6-33a9-8a58-4754c248c97a}, created = {2013-09-02T07:41:49.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Siberchicot2013}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Siberchicot, Aurélie and Julien-Laferrière, Alice and Thioulouse, Jean and Dray, Stéphane}, booktitle = {2èmes Rencontres R} }
@inproceedings{ title = {Développement de méthodes de régression multibloc pour le traitement des données d’épidémiologie vétérinaire. Des besoins statistiques des épidémiologistes au développement d’un package R}, type = {inproceedings}, year = {2013}, city = {Maison-Alfort, France}, id = {3dbb3abf-3ff1-3511-a871-24ca0d83ca31}, created = {2013-09-02T08:06:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Bougeard2013}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Bougeard, S. and Lupo, C and Chauvin, C and Fablet, C and Dray, Stéphane and Rose, N}, booktitle = {Journées de l’association pour l’étude de l’épidémiologie des maladies animales} }
@article{ title = {Functional traits reveal processes driving natural afforestation at large spatial scales.}, type = {article}, year = {2013}, pages = {e75219}, volume = {8}, websites = {http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075219}, month = {1}, id = {0821832c-86d3-3681-9c43-3b27f4d2c810}, created = {2013-09-25T07:36:03.000Z}, accessed = {2013-09-25}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Mason2013a}, private_publication = {false}, abstract = {An understanding of the processes governing natural afforestation over large spatial scales is vital for enhancing forest carbon sequestration. Models of tree species occurrence probability in non-forest vegetation could potentially identify the primary variables determining natural afforestation. However, inferring processes governing afforestation using tree species occurrence is potentially problematic, since it is impossible to know whether observed occurrences are due to recruitment or persistence of existing trees following disturbance. Plant functional traits have the potential to reveal the processes by which key environmental and land cover variables influence afforestation. We used 10,061 survey plots to identify the primary environmental and land cover variables influencing tree occurrence probability in non-forest vegetation in New Zealand. We also examined how these variables influenced diversity of functional traits linked to plant ecological strategy and dispersal ability. Mean annual temperature was the most important environmental predictor of tree occurrence. Local woody cover and distance to forest were the most important land cover variables. Relationships between these variables and ecological strategy traits revealed a trade-off between ability to compete for light and colonize sites that were marginal for tree occurrence. Biotically dispersed species occurred less frequently with declining temperature and local woody cover, suggesting that abiotic stress limited their establishment and that biotic dispersal did not increase ability to colonize non-woody vegetation. Functional diversity for ecological strategy traits declined with declining temperature and woody cover and increasing distance to forest. Functional diversity for dispersal traits showed the opposite trend. This suggests that low temperatures and woody cover and high distance to forest may limit tree species establishment through filtering on ecological strategy traits, but not on dispersal traits. This study shows that 'snapshot' survey plot data, combined with functional trait data, may reveal the processes driving tree species establishment in non-forest vegetation over large spatial scales.}, bibtype = {article}, author = {Mason, Norman W H and Wiser, Susan K and Richardson, Sarah J and Thorsen, Michael J and Holdaway, Robert J and Dray, Stéphane and Thomson, Fiona J and Carswell, Fiona E}, doi = {10.1371/journal.pone.0075219}, journal = {PLoS ONE}, number = {9} }
@article{ title = {Conference Report: Deuxièmes Rencontres R}, type = {article}, year = {2013}, pages = {164-165}, volume = {5}, websites = {http://journal.r-project.org/archive/2013-2/RJ-2013-2.pdf#page=165}, id = {ef02fa81-57f3-3a57-9a84-95dec0d5ceca}, created = {2014-01-16T16:20:10.000Z}, accessed = {2014-01-16}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Siberchicot2013a}, private_publication = {false}, bibtype = {article}, author = {Siberchicot, A and Dray, Stéphane}, journal = {The R Journal} }
@article{ title = {Development of multi-block regression analysis to process veterinary epidemiological data. From statistical needs of epidemiologists to development of R package}, type = {article}, year = {2013}, volume = {63}, id = {c63f9f46-d896-31bb-afc6-8d910aab39c1}, created = {2017-11-27T22:49:32.111Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.789Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {false}, hidden = {false}, private_publication = {true}, abstract = {The purpose of this paper is to describe the development strategy of statistical methods to be applied in the field. As an example, the development of multiblock regression methods applied to veterinary epidemiological data is described. The sequential steps in this strategy are detailed: listing of constraints to be considered, methodological development, associated indexes and design of graphical displays, testing phase with applications to numerous datasets and finally package development on the free R software to make these methods available to all potential users. An illustration of a multiblock regression method and of way how to apply it to epidemiological data in broiler chickens using the R package is presented in order to identify risk factors of losses (mortality and condemnation).}, bibtype = {article}, author = {Bougeard, Stéphanie and Lupo, C. and Chauvin, C. and Fablet, C. and Dray, Stéphane and Rose, N.}, journal = {Epidemiologie et Sante Animale} }
@article{ title = {Community ecology in the age of multivariate multiscale spatial analysis}, type = {article}, year = {2012}, pages = {257-275}, volume = {82}, websites = {http://www.esajournals.org/doi/abs/10.1890/11-1183.1}, id = {6a30d099-ab72-318a-b00b-143bf700e941}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.701Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2012}, source_type = {article}, private_publication = {false}, abstract = {Species spatial distributions are the result of population demography, behavioral traits, and species interactions in spatially heterogeneous environmental conditions. Hence the composition of species assemblages is an integrative response variable, and its variability can be explained by the complex interplay among several structuring factors. The thorough analysis of spatial variation in species assemblages may help infer processes shaping ecological communities. We suggest that ecological studies would benefit from the combined use of the classical statistical models of community composition data, such as constrained or unconstrained multivariate analyses of site-by-species abundance tables, with rapidly emerging and diversifying methods of spatial pattern analysis. Doing so allows one to deal with spatially explicit ecological models of beta diversity in a biogeographic context through the multiscale analysis of spatial patterns in original species data tables, including spatial characterization of fitted or residual variation from environmental models. We summarize here the recent progress for specifying spatial features through spatial weighting matrices and spatial eigenfunctions in order to define spatially constrained or scale-explicit multivariate analyses. Through a worked example on tropical tree communities, we also show the potential of the overall approach to identify significant residual spatial patterns that could arise from the omission of important unmeasured explanatory variables or processes.}, bibtype = {article}, author = {Dray, Stéphane and Pélissier, R and Couteron, P and Fortin, M J and Legendre, P and Peres-Neto, P R and Bellier, E and Bivand, R and Blanchet, F G and De Caceres, M and Dufour, Anne-Béatrice and Heegaard, E and Jombart, T and Munoz, F and Oksanen, J and Thioulouse, J and Wagner, H H}, journal = {Ecological Monographs}, number = {3} }
@article{ title = {Assessing species and community functional responses to environmental gradients: which multivariate methods?}, type = {article}, year = {2012}, pages = {805-821}, volume = {23}, websites = {http://doi.wiley.com/10.1111/j.1654-1103.2012.01402.x}, month = {3}, day = {19}, id = {c39d4aff-a13d-34b4-bd02-261d4309e759}, created = {2010-11-03T21:13:25.000Z}, accessed = {2012-07-13}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2020-02-11T20:44:38.185Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Kleyer2012}, source_type = {article}, private_publication = {false}, abstract = {Question: How do multivariate methods perform in relating species- and community-level trait responses to the environment? Location (1) Field data from grazed semi-natural grasslands, NE Germany; (2) artificial data. Methods: Research questions associated with trait-environment relationships were briefly reviewed and seven available methods evaluated. The main distinction between research questions is whether trait-environment relationships should be addressed at community or species level. A redundancy analysis (RDA) of mean trait values of species in a plot weighted by their abundances (CWM-RDA) is exclusively suitable for the community level. The other six methods address the species level. A double inertia analysis of two arrays (RLQ) and double canonical correspondence analysis (double CCA) use combinations of ordinations to simultaneously analyse species and trait responses to the environment. A combination of the outlying mean index with generalized additive models (OMI-GAM) predicts the response of species to environmental variables on trait gradients. RDA-RegTree first analyses species responses to the environment with RDA and then uses a regression tree to classify trait expressions according to scores of species responses on the ordination axes. Cluster regression uses cluster analyses and logistic regression to search for trait combinations with the best response to the environmental variables. This method models the distribution of functional groups on environmental gradients. All methods and data are available as R scripts. Results: All methods consistently revealed the main trait responses to environment in the field data set, namely that life history was associated with available phosphorus while grazing intensity was related to leaf C:N ratio and canopy height. At community level, CWM-RDA gave a good overview of trait-environment relationships, as also provided by the species-based methods RLQ and double CCA. OMI-GAM revealed non-linear relationships in the field data set. Field and artificial data gave that the number and stability of functional groups produced by Cluster regression and RDA-RegTree varied more strongly than RLQ, double CCA and OMI-GAM. Conclusions: Each method addresses particular ecological concepts and research questions. If a user asks for the response of average trait expressions of communities to environmental gradients, CWM-RDA may be the first choice. However, species-based methods should be applied to address questions regarding co-existence of different life histories or to assess how groups of species respond to environmental changes. The artificial data set revealed that the methods differed in sensitivity to gradient lengths and random data.}, bibtype = {article}, author = {Kleyer, Michael and Dray, Stéphane and De Bello, Francesco and Lepš, Jan and Pakeman, Robin J and Strauss, Barbara and Thuiller, Wilfried and Lavorel, Sandra}, editor = {Wildi, Otto}, doi = {10.1111/j.1654-1103.2012.01402.x}, journal = {Journal of Vegetation Science} }
@article{ title = {Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics}, type = {article}, year = {2012}, pages = {S14-S30}, volume = {93}, id = {d6ed31a5-b153-3f78-be8a-f0b223f34345}, created = {2011-12-03T11:32:44.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Peres-Neto2012}, private_publication = {false}, abstract = {Patterns in biodiversity and species coexistence are the result of multiple interacting processes including evolutionary history, trait variation, species interactions, dispersal, environmental variation, and landscape heterogeneity. Exploring patterns of biodiversity across space is perhaps the best integrative method (in contrast to the scarcity of temporal data) to interpret the influence of these multiple and interactive effects in determining community assembly, but it is still underdeveloped. Two emerging fields, metacommunity ecology and community phylogenetics, have been making relevant, though rather independent, progress toward understanding how communities are assembled in space. Our main goals were twofold. First, we described a heuristical framework to merge these two fields into "metacommunity phylogenetics." The main goal of this framework is to provide a way to think about how niche properties of species arranged across the environment and different spatial scales influence the process of community assembly. Second, we developed an analytical framework to link niche properties based on trait and phylogenetics to environmental and spatial variation. In order to assess the performance of the framework, we used extensive computer simulations of community assembly to show that the procedure is robust under a variety of scenarios.}, bibtype = {article}, author = {Peres-Neto, P R and Leibold, M.A. and Dray, Stéphane}, journal = {Ecology}, number = {8} }
@article{ title = {Predator-prey spatial game as a tool to understand the effects of protected areas on harvester-wildlife interactions}, type = {article}, year = {2012}, pages = {648-657}, volume = {22}, id = {d17f97a0-423b-39ba-a99a-71ae62bdd02c}, created = {2011-12-03T11:26:17.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Tolon2012}, private_publication = {false}, abstract = {No-take reserves are sometimes implemented for sustainable population harvesting because they offer opportunities for animals to spatially avoid harvesters, whereas harvesters can benefit in return from the reserve spillover. Here, we used the framework of predator-prey spatial games to understand how protected areas shape spatial interactions between harvesters and target species and determine animal mortality. In these spatial games, the "predator" searches for "prey" and matches their habitat use, unless it meets spatial constraints offering the opportunity for prey to avoid the mortality source. However, such prey refuges could attract predators in the surroundings, which questions the potential benefits for prey. We located, in the Geneva Basin (France), hunting dogs and wild boar Sus scrofa L. during hunting seasons with global positioning systems and very-high-frequency collars. We quantified how the proximity of the reserve shaped the matching between both habitat uses using multivariate analyses and linked these patterns to animals' mortality with a Cox regression analysis. Results showed that habitat uses by both protagonists disassociated only when hunters were spatially constrained by the reserve. In response, hunters increased hunting efforts near the reserve boundary, which induced a higher risk exposure for animals settled over the reserve. The mortality of adult wild boar decreased near the reserve as the mismatch between both habitat uses increased. However the opposite pattern was determined for younger individuals that suffered from the high level of hunting close to the reserve. The predator-prey analogy was an accurate prediction of how the protected area modified spatial relationships between harvesters and target species. Prey-searching strategies adopted by hunters around reserves strongly impacted animal mortality and the efficiency of the protected area for this harvested species. Increasing reserve sizes and/or implementing buffer areas with harvesting limitations can dampen this edge effect and helps harvesters to benefit durably from source populations of reserves. Predator-prey spatial games therefore provide a powerful theoretical background for understanding wildlife-harvester spatial interactions and developing substantial application for sustainable harvesting.}, bibtype = {article}, author = {Tolon, V and Martin, J and Dray, Stéphane and Loison, A and Fischer, C and Baubet, E}, journal = {Ecological Applications}, number = {2} }
@article{ title = {Disentangling plant trait responses to livestock grazing from spatio-temporal variation: the partial RLQ approach}, type = {article}, year = {2012}, keywords = {Covariables,Fourth-corner analysis,Namibia,Piosphere,Plant functional types,Savanna,Semi-arid rangeland,Variation partitioning}, pages = {98-113}, volume = {23}, websites = {http://doi.wiley.com/10.1111/j.1654-1103.2011.01342.x}, day = {20}, id = {239c7e67-5631-3cb8-b762-a39619951d55}, created = {2011-12-03T11:23:18.000Z}, accessed = {2011-09-26}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Wesuls2012}, private_publication = {false}, abstract = {Questions: Which plant traits consistently respond to grazing in different years and across habitat-related environmental heterogeneity? Does the proposed partial RLQ approach allow partitioning of grazing-related environmental parameters from other environmental and temporal variations? Location :Semi-arid savannas of central Namibia. Methods: We recorded nine quantitative and 12 categorical traits from 87 plant species along grazing gradients in semi-arid Namibian rangelands. We sampled from gradients in different habitat settings in 2 yr with differing total rainfall amounts. We first examined trait-environment relations with RLQ analysis. To remove confounding effects of temporal and habitat-related environmental variation on trait performance, we introduced a novel partial RLQ analysis approach. Furthermore, we used the fourth-corner statistic to quantify and test relations between traits, environmental factors and RLQ axes. Results: Habitats and years had strong influences on trait patterns. After removing environmental variation caused by habitats and years, grazing became the most influential factor on trait responses. Traits negatively correlated with increasing grazing pressure were common to perennial grasses, such as long and entire leaves, anemochorous dispersal and rhizomatous growth. Positively correlated traits were those common to herbaceous, annual plants with a prostrate-creeping habit, compound leaves, high specific leaf area (SLA) and exo- or endozoochorous dispersal. Some previously acknowledged grazing response traits, like growth form and plant height, were strongly influenced by variations in habitats and years and showed no significant correlation with grazing pressure. Conclusion: We emphasize that some traits that respond to grazing may also vary under different habitat conditions and among years, especially in highly variable environments like semi-arid savannas. When analysing trait-environment relations we recommend using approaches that partition environmental variation, particularly when applying broad sampling schemes at larger geographical scales.}, bibtype = {article}, author = {Wesuls, Dirk and Oldeland, Jens and Dray, Stéphane}, editor = {Prinzing, Andreas}, doi = {10.1111/j.1654-1103.2011.01342.x}, journal = {Journal of Vegetation Science} }
@article{ title = {How to measure and test phylogenetic signal}, type = {article}, year = {2012}, pages = {743-756}, volume = {3}, id = {016223ac-84f0-362f-b8c6-9824ba57810c}, created = {2012-02-09T14:28:06.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Munkemuller2012}, private_publication = {false}, abstract = {1. Phylogenetic signal is the tendency of related species to resemble each other more than species drawn at random from the same tree. This pattern is of considerable interest in a range of ecological and evolutionary research areas, and various indices have been proposed for quantifying it. Unfortunately, these indices often lead to contrasting results, and guidelines for choosing the most appropriate index are lacking. 2. Here, we compare the performance of four commonly used indices using simulated data. Data were generated with numerical simulations of trait evolution along phylogenetic trees under a variety of evolutionary models. We investigated the sensitivity of the approaches to the size of phylogenies, the resolution of tree structure and the availability of branch length information, examining both the response of the selected indices and the power of the associated statistical tests. 3. We found that under a Brownian motion (BM) model of trait evolution, Abouheif's Cmean and Pagel's Lambda performed well and substantially better than Moran's I and Blomberg's K. Pagel's Lambda provided a reliable effect size measure and performed better for discriminating between more complex models of trait evolution, but was computationally more demanding than Abouheif's Cmean. Blomberg's K was most suitable to capture the effects of changing evolutionary rates in simulation experiments. 4. Interestingly, sample size influenced not only the uncertainty but also the expected values of most indices, while polytomies and missing branch length information had only negligible impacts. 5. We propose guidelines for choosing among indices, depending on (a) their sensitivity to true underlying patterns of phylogenetic signal, (b) whether a test or a quantitative measure is required and (c) their sensitivities to different topologies of phylogenies. 6. These guidelines aim to better assess phylogenetic signal and distinguish it from random trait distributions. They were developed under the assumption of BM, and additional simulations with more complex trait evolution models show that they are to a certain degree generalizable. They are particularly useful in comparative analyses, when requiring a proxy for niche similarity, and in conservation studies that explore phylogenetic loss associated with extinction risks of specific clades.}, bibtype = {article}, author = {Münkemüller, Tamara and Lavergne, S and Bzeznik, B. and Dray, Stéphane and Jombart, T and Schiffers, Katja and Thuiller, Wilfried}, journal = {Methods in Ecology and Evolution} }
@article{ title = {Improved testing of species traits-environment relationships in the fourth corner problem}, type = {article}, year = {2012}, pages = {1525-1526}, volume = {93}, id = {614e292d-83e2-39ee-b216-1ec8be954c5a}, created = {2012-02-29T11:54:07.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {TerBraak2012}, private_publication = {false}, abstract = {The fourth-corner problem entails estimation and statistical testing of the relationship between species traits and environmental variables from the analysis of three data tables. In a 2008 paper, S. Dray and P. Legendre proposed and evaluated five permutation methods for statistical significance testing, including a new two-step testing procedure. However, none of these attained the correct type I error in all cases of interest. We solve this problem by showing that a small modification of their two-step procedure controls the type I error in all cases. The modification consists of adjusting the significance level from sqrt(alpha) to alpha or, equivalently, of reporting the maximum of the individual P values as the final one. The test is also applicable to the three-table ordination method RLQ.}, bibtype = {article}, author = {ter Braak, C.J.F. and Cormont, A. and Dray, Stéphane}, journal = {Ecology} }
@article{ title = {The Harttiini (Siluriformes, Loricariidae) from the Guianas: a multi-table approach to assess their diversity, evolution, and distribution}, type = {article}, year = {2012}, keywords = {- morphometry - dna,analysis - new species,barcodes - coi gene,descrip-,ecology - multiple co-inertia}, pages = {115-161}, volume = {36}, id = {a8cf8f2d-f99f-3960-9c4a-477a54115208}, created = {2012-06-07T16:36:22.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2012}, private_publication = {false}, abstract = {The Harttiini are a tribe of Loricariinae poorly characterized morphologically. Within the Guianas (French Guiana, Suriname, and Guyana), six valid species were recognized, including five Harttia, and the monotypic Harttiella crassicauda. Recent investigations conducted during the last decade by the authors and their co-workers, revealed several unidentified populations of Harttiini. Using a multivariate and multi-table approach unifying morphometry, genetics through DNA barcodes, and ecology-distribution of all populations and species, the global diversity and main evolutionary trends of this group were assessed. The separate analyses highlighted strong structures supporting the validity of three genera: Harttiella, Harttia, and Cteniloricaria, as well as nine new species (six Harttiella, two Harttia, and one Cteniloricaria), and one synonym. The combined analysis established a compromise between the preliminary ones, and revealed their common structure. This structure was found to be linked to the evolutionary history of Harttiini. Their evolution was driven toward adaptations to a definite type of biotope. These included modifications in size and shape, particularly of the caudal peduncle, depending on whether the species colonised rivers or mountainous forest creeks. A longitudinal evolutionary gradient was also highlighted in the geographical distribution of the species despite large overlaps. Notably, Harttiella possessed the greatest number of species with the smallest distribution, making each of them highly vulnerable to anthropic perturbations of their environment. Nine new species are described and a key to all species from the Guianas is proposed.}, bibtype = {article}, author = {Covain, R and Fisch-Muller, S and Montoya-Burgos, J and Mol, J.H. and Le Bail, P Y and Dray, Stéphane}, journal = {Cybium}, number = {1} }
@inproceedings{ title = {Visualisation de données multivariées: réimplémentation des fonctionnalités graphiques de la librairie ade4}, type = {inproceedings}, year = {2012}, websites = {http://r2012.bordeaux.inria.fr/}, city = {Bordeaux, France}, id = {018d5174-2f37-3ee8-a92b-b89d04ba1d4b}, created = {2012-07-17T15:53:37.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Julien-Laferriere2012}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Julien-Laferrière, Alice and Dray, Stéphane}, booktitle = {1ères Rencontres R} }
@inproceedings{ title = {Analyse de (K+1) tableaux avec le logiciel ade4. Application en épidémiologie}, type = {inproceedings}, year = {2012}, websites = {http://r2012.bordeaux.inria.fr/}, city = {Bordeaux, France}, id = {692757ce-f9bd-355e-942c-d7e27786e21c}, created = {2012-07-17T15:57:52.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Bougeard2012}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Bougeard, S. and Dray, Stéphane}, booktitle = {1ères Rencontres R} }
@inproceedings{ title = {ade4: statistical methods and graphical functions for the analysis of multivariate data}, type = {inproceedings}, year = {2012}, city = {Lyon, France}, id = {221fda36-850e-33ff-b915-b11b5a336285}, created = {2015-01-28T14:41:28.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2012a}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane and Julien-Laferrière, Alice}, booktitle = {Axe Méthodologique de l'UMR 5558, 26 April} }
@inproceedings{ title = {ade4: statistical methods and graphical functions for the analysis of multivariate data}, type = {inproceedings}, year = {2012}, city = {Lyon, France}, id = {aa190a70-cf7f-3d0f-84ca-6a8807871631}, created = {2015-01-28T14:41:28.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2012b}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane and Julien-Laferrière, Alice}, booktitle = {Statomique, 27 November} }
@article{ title = {Revisiting Guerry's data: introducing spatial constraints in multivariate analysis}, type = {article}, year = {2011}, keywords = {Autocorrelation,duality diagram,multivariate analysis,spatial weighting matrix}, pages = {2278-2299}, volume = {5}, websites = {http://dx.doi.org/10.1214/10-AOAS356}, id = {4bfcd96a-c7c9-3cf7-a6e8-8a9378427185}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2011b}, source_type = {article}, private_publication = {false}, abstract = {Standard multivariate analysis methods aim to identify and summarize the main structures in large data sets containing the description of a number of observations by several variables. In many cases, spatial information is also available for each observation, so that a map can be associated to the multivariate data set. Two main objectives are relevant in the analysis of spatial multivariate data: summarizing covariation structures and identifying spatial patterns. In practice, achieving both goals simultaneously is a statistical challenge, and a range of methods have been developed that offer trade-offs between these two objectives. In an applied context, this methodological question has been and remains a major issue in community ecology, where species assemblages (i.e., covariation between species abundances) are often driven by spatial processes (and thus exhibit spatial patterns). In this paper we review a variety of methods developed in community ecology to investigate multivariate spatial patterns. We present different ways of incorporating spatial constraints in multivariate analysis and illustrate these different approaches using the famous data set on moral statistics in France published by André-Michel Guerry in 1833. We discuss and compare the properties of these different approaches both from a practical and theoretical viewpoint.}, bibtype = {article}, author = {Dray, Stéphane and Jombart, T}, journal = {The Annals of Applied Statistics}, number = {4} }
@article{ title = {A new perspective about Moran's coefficient: spatial autocorrelation as a linear regression problem}, type = {article}, year = {2011}, pages = {127-141}, volume = {43}, id = {283371de-07e1-3422-a61f-16ae6c1fec7f}, created = {2011-04-06T12:03:00.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2011a}, private_publication = {false}, abstract = {The computation of Moran's index of spatial autocorrelation requires the definition of a spatial weighting matrix. The eigendecomposition of this doubly centered matrix (i.e., one that forces the sums of all rows and columns to equal zero) has interesting properties that have been exploited in various contexts: distribution properties of the Moran coefficient (MC), spatial filtering in linear models, generalized linear models, and multivariate analysis. In this article, this eigendecomposition is used to propose a new view of MC based on its interpretation in the simple context of linear regression. I use this interpretation to demonstrate the different properties of MC and also the inefficiency of this index in some situations involving simultaneous positive and negative spatial autocorrelation. I propose some new statistics and procedures for testing spatial autocorrelation, and conduct a simulation study to evaluate these new approaches.}, bibtype = {article}, author = {Dray, Stéphane}, journal = {Geographical Analysis} }
@article{ title = {Relationships between species feeding traits and environmental conditions in fish communities: a three-matrix approach}, type = {article}, year = {2011}, keywords = {RLQ,trait}, pages = {363-377}, volume = {21}, id = {ef713d02-b4e0-388d-8615-69d2683a0491}, created = {2011-04-06T11:56:49.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Brind'Amour2011}, private_publication = {false}, abstract = {Understanding the relationships between species biological traits and the environment is crucial to predicting the effect of habitat perturbations on fish communities. It is also an essential step in the assessment of the functional diversity. Using two complementary three-matrix approaches (fourth-corner and RLQ analyses), we tested the hypothesis that feeding-oriented traits determine the spatial distributions of littoral fish species by assessing the relationship between fish spatial distributions, fish species traits, and habitat characteristics in two Laurentian Shield lakes. Significant associations between the feeding-oriented traits and the environmental characteristics suggested that fish communities in small lakes (displaying low species richness) can be spatially structured. Three groups of traits, mainly categorized by the species spatial and temporal feeding activity, were identified. The water column may be divided in two sections, each of them corresponding to a group of traits related to the vertical distribution of the prey coupled with the position of the mouth. Lake areas of low structural complexity were inhabited by functional assemblages dominated by surface feeders while structurally more complex areas were occupied by mid-water and benthic feeders. A third group referring to the time of feeding activity was observed. Our work could serve as a guideline study to evaluate species traits × environment associations at multiple spatial scales. Our results indicate that three-matrix statistical approaches are powerful tools that can be used to study such relationships. These recent statistical approaches open up new research directions such as the study of spatially based biological functions in lakes. They also provide new analytical tools for determining, for example, the potential size of freshwater protected areas.}, bibtype = {article}, author = {Brind'Amour, A and Boisclair, D and Dray, Stéphane and Legendre, P}, journal = {Ecological Applications}, number = {2} }
@inproceedings{ title = {How can ecological status be summarized for an operational Pressures/States model ?}, type = {inproceedings}, year = {2011}, websites = {http://meetings.copernicus.org/egu2011/}, city = {Vienna, Austria}, id = {005f31a5-9beb-31d0-8be5-4f8cb893cd62}, created = {2011-09-21T15:38:01.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Lalande2011}, source_type = {inproceedings}, notes = {Poster}, private_publication = {false}, bibtype = {inproceedings}, author = {Lalande, N. and Cernesson, F and Dray, Stéphane and Tournoud, M.G. and Tormos, T. and Kosuth, T.}, booktitle = {European Geosciences Union - EGU} }
@inproceedings{ title = {Analyzing spatial multivariate structures}, type = {inproceedings}, year = {2011}, websites = {http://carme2011.agrocampus-ouest.fr/}, city = {Rennes, France}, id = {f21d206a-99f0-30b5-9332-078077544c97}, created = {2012-07-18T12:14:11.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2011}, source_type = {inproceedings}, notes = {Invited conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {International conference on Correspondence Analysis and Related Methods - CARME} }
@inproceedings{ title = {Multivariate analysis of ecological data with ade4}, type = {inproceedings}, year = {2011}, websites = {http://carme2011.agrocampus-ouest.fr/}, city = {Rennes, France}, id = {d7683115-b04a-3e7d-98eb-1615393cd0ce}, created = {2012-07-18T12:18:37.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-08-24T12:30:15.788Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2011c}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {International conference on Correspondence Analysis and Related Methods - CARME} }
@inproceedings{ title = {Linking traits to environmental variation}, type = {inproceedings}, year = {2011}, websites = {http://qcbs.ca/events/workshop-on-community-phylogenetics/}, city = {Montréal, Canada}, id = {f82d2e17-f83d-3ccf-a682-c5e383527000}, created = {2012-07-18T12:21:45.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2011d}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Workshop on community phylogenetics, 11 October} }
@article{ title = {adephylo: new tools for investigating the phylogenetic signal in biological traits}, type = {article}, year = {2010}, pages = {1907-1909}, volume = {26}, id = {0bd0bf1b-fd87-3bca-b9c7-1e44cf6eef48}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Jombart2010}, source_type = {article}, private_publication = {false}, bibtype = {article}, author = {Jombart, T and Balloux, F and Dray, Stéphane}, journal = {Bioinformatics} }
@article{ title = {The exploratory analysis of autocorrelation in animal-movement studies}, type = {article}, year = {2010}, pages = {673-681}, volume = {25}, id = {1a91cc7e-6feb-30f9-8999-794f16b4c178}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2010a}, source_type = {article}, private_publication = {false}, abstract = {Studies of animal movements have been popularized for many large and shy species by the increasing use of radio telemetry methods (VHF and GPS technologies). Data are collected with high sampling frequency, and consist of successive observations of the position of an individual animal. The statistical analysis of such data poses several problems due to the lack of independence of successive observations. However, the statistical description of the temporal autocorrelation between successive steps is rarely performed by ecologists studying the patterns of animals movements. The aim of this paper is to warn ecologists against the consequences of failing to consider this aspect. We discuss the various issues related to analyzing autocorrelated data, and show how the exploratory analysis of autocorrelation can both reveal important biological insights and help to improve the accuracy of movement models. We suggest some tools that can be used to measure, test, and adjust for temporal autocorrelation. A short ecological illustration is presented.}, bibtype = {article}, author = {Dray, Stéphane and Royer-Carenzi, M and Calenge, C}, journal = {Ecological Research} }
@article{ title = {Make love not war: when should less competitive males choose low-quality but defendable females?}, type = {article}, year = {2010}, pages = {650-661}, volume = {175}, id = {4de7f4f2-1aa0-3de1-ab9c-92263bc24ffa}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Venner2010}, source_type = {article}, private_publication = {false}, abstract = {Male choosiness for mates is an underexplored mechanism of sexual selection. A few theoretical studies suggest that males may exhibit -but only under rare circumstances- a reversed male mate choice (RMMC; i.e., highly competitive males focus on the most fecund females, while the low‐quality males exclusively pair with less fecund mates to avoid being outcompeted by stronger rivals). Here we propose a new model to explore RMMC by relaxing some of the restrictive assumptions of the previous models and by considering an extended range of factors known to alter the strength of sexual selection (males’ investment in reproduction, difference of quality between females, operational sex ratio). Unexpectedly, we found that males exhibited a reversed mate choice under a wide range of circumstances. RMMC mostly occurs when the female encounter rate is high and males devote much of their time to breeding. This condition‐dependent strategy occurs even if there is no risk of injury during the male‐male contest or when the difference in quality between females is small. RMMC should thus be a widespread yet underestimated component of sexual selection and should largely contribute to the assortative pairing patterns observed in numerous taxa.}, bibtype = {article}, author = {Venner, S and Bernstein, C and Dray, Stéphane and Bel-Venner, M C}, journal = {The American Naturalist} }
@inproceedings{ title = {Une approche multivariée pour la recherche de structures phylogénétiques dans les données biologiques}, type = {inproceedings}, year = {2010}, websites = {http://www.ecologie2010.fr/}, month = {3}, city = {Montpellier, France}, id = {006bde43-e0a0-3d35-949d-e10b6882ec74}, created = {2010-11-08T08:49:29.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Jombart2010b}, source_type = {inproceedings}, notes = {Poster}, private_publication = {false}, bibtype = {inproceedings}, author = {Jombart, T and Pavoine, S and Devillard, S and Pontier, D and Dray, Stéphane}, booktitle = {Ecologie 2010}, keywords = {phylogenie} }
@inproceedings{ title = {Analyses multivariées et mesures d'autocorrélation spatiale pour l'analyse des assemblages d'espèces}, type = {inproceedings}, year = {2010}, websites = {http://www.ecologie2010.fr/}, city = {Montpellier, France}, id = {b9a5d5a6-d2c6-3ccb-b966-2ba8ea0ba4e6}, created = {2010-11-08T08:44:13.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2010b}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane and Jombart, T}, booktitle = {Ecologie 2010}, keywords = {spatial} }
@inproceedings{ title = {Développements méthodologiques autour de l'analyse de données écologiques}, type = {inproceedings}, year = {2010}, city = {Lyon, France}, id = {f6386e7a-dd96-3343-b869-413e7f7987d4}, created = {2012-07-18T12:32:37.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2010}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Journée du PRABI, 10 November} }
@inproceedings{ title = {(Some elements of) Spatial ecological data analysis}, type = {inproceedings}, year = {2010}, city = {Lyon, France}, id = {38cc568c-c94e-3759-8bd4-c7a8e8449fe3}, created = {2012-07-18T12:43:44.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2010c}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Séminaire du DIPEE, 27 January} }
@inproceedings{ title = {Some methodological developments around the spatial weighting matrix in ecology}, type = {inproceedings}, year = {2010}, city = {Paris, France}, id = {ba40a0a3-36da-3a5c-bf3d-0fea0ade3ee6}, created = {2012-07-18T12:49:09.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2010d}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Réunion du réseau MIA Modèles Hiérarchiques Spatiaux, 27 January} }
@article{ title = {Corrigendum to "Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes" Mol. Phylogenet. Evol. 46 (2008) 986-1002 (DOI:10.1016/j.ympev.2007.12.015)}, type = {article}, year = {2010}, volume = {55}, id = {445f2a5f-6935-37bf-a8fd-d0722b2618c6}, created = {2017-11-27T22:49:32.066Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.561Z}, read = {false}, starred = {false}, authored = {true}, confirmed = {false}, hidden = {false}, private_publication = {true}, bibtype = {article}, author = {Covain, R. and Dray, Stéphane and Fisch-Muller, S. and Montoya-Burgos, J.I.}, doi = {10.1016/j.ympev.2009.10.036}, journal = {Molecular Phylogenetics and Evolution}, number = {2} }
@inproceedings{ title = {Les Harttiini (Siluriformes, Loricariidae) des Guyanes : phylogénie et évolution des formes ou variation sur un même thème.}, type = {inproceedings}, year = {2009}, city = {Paris, France}, id = {e8ff05b1-9a0b-3a64-8375-5cfb399dd799}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2009b}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Covain, R and Fisch-Muller, S and Montoya-Burgos, J and Mol, J and Le Bail, P Y and Dray, Stéphane}, booktitle = {RIF 2009 (4e Rencontres de l'Ichtyologie en France)} }
@inproceedings{ title = {Extracting phylogenetic signal in morphometric data to complete molecular phylogenies: a case study on Harttiini (Siluriformes, Loricariidae) from the Guianas}, type = {inproceedings}, year = {2009}, city = {Marseille, France}, id = {d3eb49f4-8a8f-3e08-a414-d677d9359bc7}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2009}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Covain, R and Fisch-Muller, S and Montoya-Burgos, J and Mol, J and Le Bail, P Y and Dray, Stéphane}, booktitle = {Evolutionary Biology Meeting} }
@article{ title = {Responding to spatial and temporal variations in predation risk: space use of a game species in a changing landscape of fear}, type = {article}, year = {2009}, pages = {1129-1137}, volume = {87}, id = {e6bb716c-14a0-3119-9d92-e6bbcb928eb8}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Tolon2009}, source_type = {article}, private_publication = {false}, abstract = {Predators generate a "landscape of fear" within which prey can minimize the risk of predation by selecting low-risk areas. Depending on the spatial structure of this "landscape", i.e., whether it is coarse- or fine-grained, prey may respond to increased risk by shifting their home ranges or by fine-scale redistributions within these ranges, respectively. We studied how wild boar (Sus scrofa L., 1758) responded to temporal changes in risk in hunted areas (risky habitat) surrounding a nature reserve (refuge habitat). Animals with home ranges "in contact" with the reserve during the low-risk season were the only ones to shift toward the refuge when the risk increased. These shifts occurred at two temporal scales in response to the increased risk during the daytime and during the hunting season. Whereas animals not influenced by the reserve found food and shelter in forest during the hunting season, shifts to the refuge area were detrimental to the rather scarce forest areas in the reserve. This confirms that spatiotemporal changes in risk are major drivers of animal distribution when predation strongly limits their fitness. Their response is, however, scale-dependent and reflects at the individual level the perceived structure of their "landscape of fear".}, bibtype = {article}, author = {Tolon, V and Dray, Stéphane and Loison, A and Zeileis, A and Fischer, C and Baubet, E}, journal = {Canadian Journal of Zoology} }
@article{ title = {The concept of animals trajectories from a data analysis perspective}, type = {article}, year = {2009}, pages = {34-41}, volume = {4}, id = {19219653-e59f-32e8-9aad-29bf05fd35ba}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Calenge2009}, source_type = {article}, private_publication = {false}, abstract = {The Global Positioning System (GPS) has been increasingly used during the past decade to monitor the movements of free-ranging animals. This technology allows to automatically relocate fitted animals, which often results into a high-frequency sampling of their trajectory during the study period. However, depending on the objective of trajectory analysis, this study may quickly become difficult, due to the lack of well designed computer programs. For example, the trajectory may be built by several "parts" corresponding to different behaviours of the animal, and the aim of the analysis could be to identify the different parts, and thereby the different activities, based on the properties of the trajectory. This complex task needs to be performed into a flexible computing environment, to facilitate exploratory analysis of its properties. In this paper, we present a new class of object of the R software, the class "ltraj" included in the package adehabitat, allowing the analysis of animals' trajectories. We developed this class of data after an extensive review of the literature on the analysis of animal movements. This class of data facilitates the computation of descriptive parameters of the trajectory (such as the relative angles between successive moves, distance between successive relocations, etc.), graphical exploration of these parameters, as well a numerous tests and analyses developed in the literature (first passage time, trajectory partitioning, etc.). Finally, this package also contains numerous examples of animal trajectories, and a working example illustrating the use of the package.}, bibtype = {article}, author = {Calenge, C and Dray, Stéphane and Royer-Carenzi, M}, journal = {Ecological Informatics} }
@article{ title = {Finding essential scales of spatial variation in ecological data: a multivariate approach}, type = {article}, year = {2009}, pages = {161-168}, volume = {32}, id = {8dcdf02f-de13-3972-b3f9-d260853b7e46}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.428Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Jombart2009}, source_type = {article}, private_publication = {false}, abstract = {The identification of spatial structures is a key step in understanding the ecological processes structuring the distribution of organisms. Spatial patterns in species distributions result from a combination of several processes occuring at different scales: identifying these scales is thus a crucial issue. Recent studies have proposed a new family of spatial predictors (PCNM: principal coordinates of neighbours matrices; MEMs: Moran's eigenvectors maps) that allow for modelling of spatial variation on different scales. To assess the multi-scale spatial patterns in multivariate data, these variables are often used as predictors in constrained ordination methods. However, the selection of the appropriate spatial predictors is still troublesome, and the identification of the main scales of spatial variation remains an open question. This paper presents a new statistical tool to tackle this issue: the multi-scale pattern analysis (MSPA). This ordination method uses MEMs to decompose ecological variability into several spatial scales and then summarizes this decomposition using graphical representations. A canonical form of MSPA can also be used to assess the spatial scales of the species-environment relationships. MSPA is compared to constrained ordination using simulated data, and illustrated using the famous oribatid mites dataset. The method is implemented in the free software R.}, bibtype = {article}, author = {Jombart, T and Dray, Stéphane and Dufour, Anne-Béatrice}, journal = {Ecography} }
@inproceedings{ title = {Phylogeny and evolution of shapes: a new approach to predict phylogenetic positions of missing taxa}, type = {inproceedings}, year = {2009}, city = {Montpellier, France}, id = {82cd0526-eb83-37d6-a9c8-5b8b25b19297}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2009a}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Covain, R and Fisch-Muller, S and Montoya-Burgos, J and Mol, J and Le Bail, P Y and Dray, Stéphane}, booktitle = {Symposium de Morphométrie et Evolution des Formes} }
@article{ title = {Unexpected male choosiness for mates in a spider}, type = {article}, year = {2008}, pages = {77-82}, volume = {275}, id = {df2f3108-5654-34fd-8f47-1384c0330ab6}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Bel-Venner2008}, source_type = {article}, private_publication = {false}, abstract = {Sexual selection theory traditionally considers choosiness for mates to be negatively related to intra-sexual competition. Males were classically considered to be the competing, but not the choosy, sex. However, evidence of male choosiness is now accumulating. Male choosiness is expected to increase with an individual’s competitive ability, and to decrease as intra-sexual competition increases. However, such predictions have never been tested in field conditions. Here, we explore male mate choice in a spider by studying size-assortative pairing in two natural sites that strongly differ in the level of male–male competition. Unexpectedly, our results demonstrate that mate choice shifts from opportunism to high selectivity as competition between males increases. Males experiencing weak competition did not exhibit size-related mating preferences. By contrast, when competition was intense we found strong size-assortative pairing due to male choice: while larger, more competitive males preferentially paired with larger, more fecund females, smaller males chose smaller females. Thus, we show that mating preferences of males vary with their competitive ability. The distinct preferences exhibited by males of different sizes seem to be an adaptive response to the lower reproductive opportunities arising from increased competition between males.}, bibtype = {article}, author = {Bel-Venner, M C and Dray, Stéphane and Allainé, Dominique and Menu, F and Venner, S}, journal = {Proceedings of the Royal Society of London Series B - Biological Sciences} }
@article{ title = {On the number of principal components: A test of dimensionality based on measurements of similarity between matrices}, type = {article}, year = {2008}, pages = {2228-2237}, volume = {52}, id = {d4cf9ad3-8bff-335b-b4cf-658153d424bc}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2008b}, source_type = {article}, private_publication = {false}, abstract = {An important problem in principal component analysis (PCA) is the estimation of the correct number of components to retain. PCA is most often used to reduce a set of observed variables to a new set of variables of lower dimensionality. The choice of this dimensionality is a crucial step for the interpretation of results or subsequent analyses, because it could lead to a loss of information (underestimation) or the introduction of random noise (overestimation). New techniques are proposed to evaluate the dimensionality in PCA. They are based on similarity measurements, singular value decomposition and permutation procedures. A simulation study is conducted to evaluate the relative merits of the proposed approaches. Results showed that one method based on the RV coefficient is very accurate and seems to be more efficient than other existing approaches.}, bibtype = {article}, author = {Dray, Stéphane}, journal = {Computational Statistics and Data Analysis} }
@article{ title = {Analyzing or explaining beta diversity? Comment.}, type = {article}, year = {2008}, pages = {3227-3332}, volume = {89}, id = {fbf6bb31-fbb0-31e2-b84b-9615022bee81}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Pelissier2008}, source_type = {article}, private_publication = {false}, bibtype = {article}, author = {Pélissier, R and Couteron, P and Dray, Stéphane}, journal = {Ecology} }
@article{ title = {Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes}, type = {article}, year = {2008}, pages = {986-1002}, volume = {46}, id = {6010b84c-96fd-35f6-9275-9491653b6be1}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2008}, source_type = {article}, private_publication = {false}, abstract = {With the increase of laboratory facilities, molecular phylogenies are playing a predominant role in evolutionary analyses. However, understanding the evolution of morphological traits remains essential for a comprehensive view of the evolution of a group. Here we present a new approach based on co-inertia analysis for identifying characters which variations are dependent to the phylogeny, a prerequisite for analyzing the evolution of characters. Our approach has the advantage of treating the full data set at once, including qualitative and quantitative variables. It provides a graphical output giving the contribution of each variable to the co-structure, allowing a direct discrimination among phylogenetically dependent and independent variables. We have implemented this approach in deciphering the evolution of morphological traits in a highly specialized group of Neotropical catfishes: the Loricariinae. We have first inferred a molecular phylogeny of this group based on the 12S and 16S mitochondrial genes. The resulting phylogeny indicated that the subtribe Harttiini was restricted to the single genus Harttia, and within the subtribe Loricariini, two sister subtribes were distinguished, Sturisomina (new subtribe), and Loricariina. Among Loricariina, the morphological groups Loricariichthys and Loricaria + Pseudohemiodon were confirmed. The co-inertia analysis highlighted a strong relationship between the morphological and the genetic data sets, and identified three quantitative and eight qualitative variables linked to the phylogeny. The evolution of quantitative variables was assessed using the orthogram method and showed a major punctual event in the evolution of the number of caudal-fin rays, and a more gradual pattern of evolution of the number of teeth along the phylogeny. The evolution of qualitative variables was inferred using ancestral states reconstructions and highlighted parallel patterns of evolution in characters linked to the mouth, suggesting co-evolution of the traits for adapting to divergent substrates.}, bibtype = {article}, author = {Covain, R and Dray, Stéphane and Fisch-Muller, S and Montoya-Burgos, J}, journal = {Molecular Phylogenetics and Evolution}, number = {3} }
@article{ title = {Testing the species traits-environment relationships: the fourth-corner problem revisited}, type = {article}, year = {2008}, pages = {3400-3412}, volume = {89}, id = {88e9f6be-f800-360e-9da5-5f6285d611df}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2008a}, source_type = {article}, folder_uuids = {4afa5ac8-d8d6-102e-ac9a-0024e85ead87}, private_publication = {false}, abstract = {Functional ecology aims at determining the relationships between species traits and environmental variables in order to better understand biological processes in ecosystems. From a methodological point of view, this biological objective calls for a method linking three data matrix tables: a table L with abundance or presence-absence values for species at a series of sites, a table R with variables describing the environmental conditions of the sites, and a table Q containing traits (e.g., morphological or behavioral attributes) of the species. Ten years ago, the fourth-corner method was proposed to measure and test the relationships between species traits and environmental variables using tables R, L, and Q simultaneously. In practice, this method is rarely used. The major reasons for this lack of interest are the restriction of the original method and program to presence-absence data in L and to the analysis of a single trait and a single environmental variable at a time. Moreover, ecologists often have problems in choosing a permutation model among the four originally proposed. In this paper, we revisit the fourth-corner method and propose improvements to the original approach. First, we present an extension to measure the link between species traits and environmental variables when the ecological community is described by abundance data. A new multivariate fourth-corner statistic is also proposed. Then, using numerical simulations, we discuss and evaluate the existing testing procedures. A new two-step testing procedure is presented. We hope that these elements will help ecologists use the best possible methodology to analyze this type of ecological problem.}, bibtype = {article}, author = {Dray, Stéphane and Legendre, P}, journal = {Ecology}, keywords = {RLQ,trait} }
@article{ title = {Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation}, type = {article}, year = {2008}, pages = {45-56}, volume = {19}, id = {5ec35be8-d9ab-3ee6-b90f-53c25bddf37e}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2008}, source_type = {article}, private_publication = {false}, abstract = {Question: Are there spatial structures in the composition of plant communities? Methods: Identification and measurement of spatial structures is a topic of great interest in plant ecology. Univariate measurements of spatial autocorrelation such as Moran's I and Geary's c are widely used, but extensions to the multivariate case (i.e. multi-species) are rare. Here, we propose a multivariate spatial analysis based on Moran's I (MULTISPATI) by introducing a row-sum standardized spatial weight matrix in the statistical triplet notation. This analysis, which is a generalization of Wartenberg's approach to multivariate spatial correlation, would imply a compromise between the relations among many variables (multivariate analysis) and their spatial structure (autocorrelation). MULTISPATI approach is very flexible and can handle various kinds of data (quantitative and/or qualitative data, contingency tables). A study is presented to illustrate the method using a spatial version of Correspondence Analysis. Location: Territoire d'Etude et d'Expérimentation de Trois-Fontaines (eastern France). Results: Ordination of vegetation plots by this spatial analysis is quite robust with reference to rare species and highlights spatial patterns related to soil properties.}, bibtype = {article}, author = {Dray, Stéphane and Saïd, S and Débias, F}, journal = {Journal of Vegetation Science} }
@inproceedings{ title = {Multi-scale assessment of the functional relationships between species traits and environmental conditions for littoral fish communities}, type = {inproceedings}, year = {2007}, city = {Montréal, Canada}, id = {091f2f70-f9ab-3381-82da-2f1dc86fd1fc}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Brind'Amour2007a}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Brind'Amour, A and Boisclair, D and Dray, Stéphane and Legendre, P}, booktitle = {60th Canadian Conference for Fisheries Research} }
@article{ title = {Testing sexual segregation and aggregation: old ways are best}, type = {article}, year = {2007}, pages = {3202-3208}, volume = {88}, id = {f8823b35-4cb7-3a01-b5b8-9548b3061001}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Bonenfant2007}, source_type = {article}, private_publication = {false}, abstract = {The study of sexual segregation has received increasing attention over the last two decades. Several hypotheses have been proposed to explain the existence of sexual segregation, such as the "predation risk hypothesis", the "forage selection hypothesis", and the "activity budget hypothesis". Testing which hypothesis drives sexual segregation is hampered, however, by the lack of consensus regarding a formal measurement of sexual segregation. By using a derivation of the well-known chi-square (here called the sexual segregation and aggregation statistic [SSAS]) instead of existent segregation coefficients, we offer a reliable way to test for temporal variation in the occurrence of sexual segregation and aggregation, even in cases where a large proportion of animals are observed alone. A randomization procedure provides a test for the null hypothesis of independence of the distributions of males and females among the groups. The usefulness of SSAS in the study of sexual segregation is demonstrated with three case studies on ungulate populations belonging to species with contrasting life histories and annual grouping patterns (isard, red deer, and roe deer). The existent segregation coefficients were unreliable since, for a given value, sexual segregation could or could not occur. Similarly, the existent segregation coefficients performed badly when males and females aggregated. The new SSAS was not prone to such limitations and allowed clear conclusions regarding whether males and females segregate, aggregate, or simply mix at random applicable to all species.}, bibtype = {article}, author = {Bonenfant, C and Gaillard, J M and Dray, Stéphane and Loison, A and Royer, M and Chessel, D}, journal = {Ecology} }
@inproceedings{ title = {Multi-scale assessment of the functional relationships between species traits and environmental conditions for littoral fish communities}, type = {inproceedings}, year = {2007}, city = {Baltimore, USA}, id = {034f2fa2-c6ad-3c1c-b9df-8d1a4112fa9b}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Brind'Amour2007}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Brind'Amour, A and Boisclair, D and Dray, Stéphane and Legendre, P}, booktitle = {Early Career Scientists Conference: New Frontiers in Marine Science} }
@article{ title = {The ade4 package - II: Two-table and K-table methods}, type = {article}, year = {2007}, pages = {47-52}, volume = {7}, id = {3bfb7317-4f8e-3072-9724-d8a31bcc585d}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2019-03-01T08:37:11.424Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2007a}, source_type = {article}, private_publication = {false}, bibtype = {article}, author = {Dray, Stéphane and Dufour, Anne-Béatrice and Chessel, D}, journal = {R News}, number = {2} }
@article{ title = {Interactive multivariate data analysis in R with the ade4 and ade4TkGUI packages}, type = {article}, year = {2007}, pages = {1-14}, volume = {22}, id = {1ad36e4e-e7db-35cf-b953-f8f13e366557}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Thioulouse2007}, source_type = {article}, private_publication = {false}, abstract = {ade4 is a multivariate data analysis package for the R statistical environment, and ade4TkGUI is a Tcl/Tk graphical user interface for the most essential methods of ade4. Both packages are available on CRAN. An overview of ade4TkGUI is presented, and the pros and cons of this approach are discussed. We conclude that command line interfaces (CLI) and graphical user interfaces (GUI) are complementary. ade4TkGUI can be valuable for biologists and particularly for ecologists who are often occasional users of R. It can spare them having to acquire an in-depth knowledge of R, and it can help first time users in a first approach.}, bibtype = {article}, author = {Thioulouse, J and Dray, Stéphane}, journal = {Journal of Statistical Software}, number = {5} }
@article{ title = {The ade4 package: implementing the duality diagram for ecologists}, type = {article}, year = {2007}, pages = {1-20}, volume = {22}, id = {7d4a50cc-2ede-3c40-ad13-f6f2ae79df19}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2007}, source_type = {article}, private_publication = {false}, abstract = {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 "Analyse des Données" and is based on the use of the duality diagram. We present the theory of the duality diagram and discuss its implementation in ade4. Classes and main functions are presented. An example is given to illustrate the ade4 philosophy.}, bibtype = {article}, author = {Dray, Stéphane and Dufour, A B}, journal = {Journal of Statistical Software}, number = {4} }
@inproceedings{ title = {"Reserve effect" on the space use of game mammals: the case of wild boar}, type = {inproceedings}, year = {2007}, city = {Siena, Italy}, id = {939c919f-9d8a-3cf3-891a-ea06dfea710d}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Tolon2007}, source_type = {inproceedings}, notes = {Poster}, private_publication = {false}, bibtype = {inproceedings}, author = {Tolon, V and Baubet, E and Dray, Stéphane and Fischer, C}, booktitle = {Vth European Mammalogy Congress} }
@inproceedings{ title = {Morphological and phylogenetic study of the subfamily Loricariinae (Siluriformes, Loricariidae)}, type = {inproceedings}, year = {2006}, city = {Genève, Suisse}, id = {ce002860-3556-3ee3-95fa-bdc1fb153fab}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2006a}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Covain, R and Dray, Stéphane and Fisch-Muller, S}, booktitle = {Biology06} }
@article{ title = {Spatial modeling: a comprehensive framework for principal coordinate analysis of neighbor matrices (PCNM)}, type = {article}, year = {2006}, pages = {483-493}, volume = {196}, id = {1a08f733-d14a-330e-9438-b33253e6730a}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2006}, source_type = {article}, short_title = {Spatial modeling: a comprehensive framework for pr}, private_publication = {false}, abstract = {Spatial structures of ecological communities may originate either from the dependence of community structure on environmental variables or/and from community-based processes. In order to assess the importance of these two sources, spatial relationships must be explicitly introduced into statistical models. Recently, a new approach called principal coordinates of neighbour matrices (PCNM) has been proposed to create spatial predictors that can be easily incorporated into regression or canonical analysis models, providing a flexible tool especially when contrasted to the family of autoregressive models and trend surface analysis, which are of common use in ecological and geographical analysis. In this paper, we explore the theory of the PCNM approach and demonstrate how it is linked to spatial autocorrelation structure functions. The method basically consists of diagonalizing a spatial weighting matrix, then extracting the eigenvectors that maximize the Moran's index of autocorrelation. These eigenvectors can then be used directly as explanatory variables in regression or canonical models. We propose improvements and extensions of the original method, and illustrate them with examples that will help ecologists choose the variant that will better suit their needs.}, bibtype = {article}, author = {Dray, Stéphane and Legendre, P and Peres-Neto, P R}, journal = {Ecological Modelling}, keywords = {MEM,Spatial} }
@inproceedings{ title = {Analyse morphologique et phylogénétique de la sous famille des Loricariinae (Siluriformes, Loricariidae)}, type = {inproceedings}, year = {2006}, city = {Paris, France}, id = {82182053-5728-3c02-a827-646161ad6593}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Covain2006}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Covain, R and Montoya-Burgos, J and Dray, Stéphane and Fisch-Muller, S}, booktitle = {RIF 2006 (3e Rencontres de l'ichtyologie en France)} }
@article{ title = {Resource partitioning in a grazer guild feeding on a multilayer diatom mat}, type = {article}, year = {2006}, pages = {800-810}, volume = {25}, id = {2589530b-8af1-3622-99d0-5b552b774635}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Tall2006}, source_type = {article}, short_title = {Diet patterns of a benthic community of grazers on}, folder_uuids = {4afa5ac8-d8d6-102e-ac9a-0024e85ead87}, private_publication = {false}, abstract = {The gut contents of a guild of invertebrate grazers inhabiting the moss Fontinalis and feeding on epiphytic diatoms in a small Que´bec stream were analyzed to characterize resource partitioning and food selection. A multivariate approach (RLQ analysis coupled with a revised version of 4th-corner analysis) identified distinct diet patterns among co-occurring grazers. These patterns were mainly explained by differential ingestion of diatoms that differed in their spatial positions within the multilayered periphyton mat. When the size range of available diatoms was large, diet differences were partly explained by diatom size. Comparison of diatoms in grazer guts with diatoms available in the environment indicated selective feeding in different levels of the periphyton mat by grazers. Some grazers (scrapers) fed preferentially on tightly attached diatoms, whereas others (surfers) favored overstory diatoms. Spatial segregation of feeding within the periphyton mat by members of the grazer guild was more evident in a period of potential resource limitation (July) than when food was abundant (May). Our results suggest that all layers/growth forms in the diatom mat are used, resulting in spatial partitioning of the resource when considering the entire grazer community. Therefore, foraging theories already established for other ecosystems are confirmed in the unique context of stream benthos.}, bibtype = {article}, author = {Tall, Laure and Cattaneo, Antonella and Cloutier, L and Dray, Stéphane and Legendre, P}, journal = {Journal of the North American Benthological Society}, keywords = {RLQ,trait} }
@inproceedings{ title = {Impact of hunting activities on the spatial behaviour of the wild boar: attractiveness of safe areas}, type = {inproceedings}, year = {2006}, city = {Kykkos, Cyprus}, id = {5c9687a6-7888-3dfc-bb8a-80467936c0e6}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Tolon2006}, source_type = {inproceedings}, notes = {Poster}, private_publication = {false}, bibtype = {inproceedings}, author = {Tolon, V and Baubet, E and Dray, Stéphane and Fischer, C and Hebeisen, C and Dobremez, J F}, booktitle = {VIth International Symposium on Wild Boar} }
@article{ title = {Variation partitioning of species data matrices: estimation and comparison of fractions}, type = {article}, year = {2006}, pages = {2614-2625}, volume = {87}, id = {373d2091-fa38-37c5-84c1-4278db5f52b0}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Peres-Neto2006a}, source_type = {article}, folder_uuids = {7e415411-ab1b-4ef7-9523-01b20e85991d}, private_publication = {false}, abstract = {Establishing relationships between species distributions and environmental characteristics is a major goal in the search for forces driving species distributions. Canonical ordinations such as redundancy analysis and canonical correspondence analysis are invaluable tools for modeling communities through environmental predictors. They provide the means for conducting direct explanatory analysis in which the association among species can be studied according to their common and unique relationships with the environmental variables and other sets of predictors of interest, such as spatial variables. Variation partitioning can then be used to test and determine the likelihood of these sets of predictors in explaining patterns in community structure. Although variation partitioning in canonical analysis is routinely used in ecological analysis, no effort has been reported in the literature to consider appropriate estimators so that comparisons between fractions or, eventually, between different canonical models are meaningful. In this paper, we show that variation partitioning as currently applied in canonical analysis is biased. We present appropriate unbiased estimators. In addition, we outline a statistical test to compare fractions in canonical analysis. The question addressed by the test is whether two fractions of variation are significantly different from each other. Such assessment provides an important step toward attaining an understanding of the factors patterning community structure. The test is shown to have correct Type I error rates and good power for both redundancy analysis and canonical correspondence analysis.}, bibtype = {article}, author = {Peres-Neto, P R and Legendre, P and Dray, Stéphane and Borcard, D}, journal = {Ecology}, keywords = {R2} }
@inproceedings{ title = {Spatial modeling: a comprehensive framework for distance-based eigenvector maps (DBEM)}, type = {inproceedings}, year = {2005}, websites = {http://www.esa.org/montreal/}, city = {Montréal, Canada}, id = {a53ad940-f50d-3475-bd5f-b8c3d9b5b6e9}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2005}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {90th Annual Meeting of ESA}, keywords = {Multivarié,Spatial} }
@inproceedings{ title = {Variation partitioning of species data matrices: estimation and comparison of fractions}, type = {inproceedings}, year = {2005}, websites = {http://www.esa.org/montreal/}, city = {Montréal, Canada}, id = {d2f5a7c5-bb2c-38b4-a2d1-6e4550bda012}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Peres-Neto2005}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Peres-Neto, P R and Legendre, P and Dray, Stéphane and Borcard, D}, booktitle = {90th Annual Meeting of ESA}, keywords = {R2} }
@article{ title = {Coupling principal component analysis and GIS to map deer habitats}, type = {article}, year = {2005}, pages = {363-370}, volume = {11}, id = {eec86a32-4b81-30fc-967c-c17e736bdc9d}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Pettorelli2005}, source_type = {article}, private_publication = {false}, abstract = {We aimed to define at a relevant scale the spatial pattern of major vegetation types available to deer in order to characterise habitat quality variations within our population area. We analysed data on the timber stand and the shrub layer collected in 1993 in the 2,614 ha Chizé reserve in western France. Multidimensional analyses (Principal Component Analysis and biplot) and a Geographic Information System (GIS) were used to extract most of the variation in vegetation data collected at the 4-ha resolution. At the timber stand level, two vegetation types occurred within the reserve: an oak Quercus sp. stand in the north, and a beech Fagus sylvatica stand in the south. This classification accounted for 29.6% of the total variability of the timber stand data base. At the shrub layer scale, three vegetation types were distinguished: hornbeam Carpinus betulus dominated coppices in the northeast part of the oak stand, maple Acer sp. dominated coppices in the northwest part of the oak stand, and no shrub layer in the beech stand in the south. This classification accounted for 32% of the total variability of the shrub layer data base. The coupled use of multivariate analysis and GIS allowed us to assess classification of forest habitats and appears promising for use in wildlife management and research purposes. This simple and robust tool allows users to account for site variability, and can provide satisfactory spatial representations of habitat potential at multiple scales.}, bibtype = {article}, author = {Pettorelli, N and Dray, Stéphane and Maillard, D}, journal = {Wildlife Biology} }
@inproceedings{ title = {Taking into account spatial dependence in multivariate analysis: a generalization of Wartenberg's multivariate spatial correlation}, type = {inproceedings}, year = {2005}, month = {6}, day = {27}, city = {Toulouse, France}, id = {054c1540-baeb-3f7d-9988-c48217b6590b}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2005a}, source_type = {inproceedings}, notes = {Invited conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Spatial Econometrics and Statistics Workshop} }
@inproceedings{ title = {Two solutions to the fourth corner problem}, type = {inproceedings}, year = {2004}, city = {Montréal, Canada}, id = {acc7336d-3f9d-30c8-8eef-ae9b1ba9fde7}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Legendre2004}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Legendre, P and Dray, Stéphane}, booktitle = {Psychology Department, McGill University, 30 March} }
@inproceedings{ title = {Nouvelles méthodes d'analyse spatiale multivariée de données incomplètes}, type = {inproceedings}, year = {2004}, city = {Montréal, Canada}, department = {Département de Bioinformatique, UQAM}, id = {93e7126b-6d06-3434-ae5b-1b94c1d35b83}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2004}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Département de Bioinformatique, UQAM, 10 November} }
@misc{ title = {Cartographie et analyse de données multivariées}, type = {misc}, year = {2003}, websites = {http://www.iag.asso.fr/articles/multivariees.pdf}, institution = {Institut d’Analyse Géographique}, id = {0f03d384-bd96-395c-a0a7-497fd9af25d6}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2003}, source_type = {techreport}, private_publication = {false}, abstract = {L’identification de structures spatiales induisant plusieurs variables est une problématique récurrente dans de nombreux domaines d’application. Cet article présente quelques aspects permettant la prise en compte de l’espace lors de l’analyse de données multivariées. Une illustration basée sur des données socio-économiques est proposée.}, bibtype = {misc}, author = {Dray, Stéphane} }
@article{ title = {Procrustean co-inertia analysis for the linking of multivariate data sets}, type = {article}, year = {2003}, pages = {110-119}, volume = {10}, id = {ad1e8af3-8176-3787-921b-204f6a022ac2}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2003d}, source_type = {article}, short_title = {Procrustean co-inertia analysis for the linking of}, private_publication = {false}, abstract = {Procrustes analysis is a method for fitting a set of points to another. These two sets of points are often defined by the measurements of two sets of variables for the same individuals (e.g., measurements of species abundances and environmental variables at the same sites). We present a solution for graphical representation of the results of procrustes analysis when the number of variables in each of the two datasets exceeds two. This method is named procrustean co-inertia analysis because it is based on the joint use of procrustes analysis and co-inertia analysis, which is a coupling method for finding linear combinations of two sets of variables of maximal covariance. It provides better graphical representation of the concordance between the two datasets than classical co-inertia analysis. Moreover, distance matrices can be introduced in the analysis to improve its ecological meaning. Lastly, a randomization test equivalent to PROTEST is proposed as an alternative to the Mantel test. An ecological example is presented to illustrate the method.}, bibtype = {article}, author = {Dray, Stéphane and Chessel, D and Thioulouse, J}, journal = {Ecoscience}, number = {1}, keywords = {Co-Inertie,Procuste,distance} }
@inproceedings{ title = {Couplage de données issues de deux plans d'échantillonnage distincts d'un même espace}, type = {inproceedings}, year = {2003}, pages = {435-438}, city = {Lyon, France}, id = {3144e7ef-69e9-3394-9b6a-4a505d90be35}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2003e}, source_type = {inproceedings}, short_title = {Couplage de données issues de deux plans d'échanti}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {XXXVèmes journées de statistiques}, keywords = {Multivarié,RLQ,Spatial} }
@inproceedings{ title = {Analyse spatialisée de données écologiques multivariées}, type = {inproceedings}, year = {2003}, city = {Montréal, Canada}, id = {9093a12b-3b7f-3e84-af57-bee39bf6c43a}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2003a}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Département des Sciences biologiques, Université de Montréal, 10 November} }
@article{ title = {Co-inertia analysis and the linking of ecological data tables}, type = {article}, year = {2003}, pages = {3078-3089}, volume = {84}, id = {d89dec49-9e6c-3a73-85a9-b3089af09fb6}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2003c}, source_type = {article}, short_title = {Co-inertia analysis and the linking of ecological }, private_publication = {false}, abstract = {Ecological studies often require studying the common structure of a pair of data tables. Co-inertia analysis is a multivariate method for coupling two tables. It is often neglected by ecologists who prefer the widely used methods of redundancy analysis and canonical correspondence analysis. We present the co-inertia criterion for measuring the adequacy between two data sets. Co-inertia analysis is based on this criterion as are canonical correspondence analysis or canonical correlation analysis, but the latter two have additional constraints. Co-inertia analysis is very flexible and allows many possibilities for coupling. Co-inertia analysis is suitable for quantitative and/or qualitative or fuzzy environmental variables. Moreover, various weighting of sites and various transformations and/or centering of species data are available for this method. Hence, more ecological considerations can be taken into account in the statistical procedures. Moreover, the principle of this method is very general and can be easily extended to the case of distance matrices or to the case of more than two tables. Simulated ecological data are used to compare the co-inertia approach with other available methods.}, bibtype = {article}, author = {Dray, Stéphane and Chessel, D and Thioulouse, J}, journal = {Ecology} }
@article{ title = {Spatial variation in springtime food resources influences the winter body mass of roe deer fawn}, type = {article}, year = {2003}, pages = {363-369}, volume = {137}, id = {67af233b-98fe-3fba-a711-b1255d35c98b}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Pettorelli2003}, source_type = {article}, short_title = {Spatial variation in springtime food resources inf}, private_publication = {false}, abstract = {It is well established that the dynamics of mammalian populations vary in time, in relation to density and weather, and often in interaction with phenotypic differences (sex, age and social status). Habitat quality has recently been identified as another significant source of individual variability in vital rates of deer, including roe deer where spatial variations in fawn body mass were found to be only about a tenth of temporal variations. The approach used was to classify the habitat into blocks a priori, and to analyse variation in animal performance among the predefined areas. In a fine-grained approach, here we use data collected over 24 years on 1,235 roe deer fawns captured at known locations and the plant species composition sampled in 2001 at 578 sites in the Chizé forest to determine the spatial structure at a fine scale of both vegetation and winter body mass of fawns, and then to determine links between the two. Space and time played a nearly equal role in determining fawn body masses of both sexes, each accounting for about 20% of variance and without any interaction between them. The spatial distribution of fawn body mass was perennial over the 24 years considered and predicted values showed a 2 kg range according to location in the reserve, which is much greater than suggested in previous work and is enough to have strong effects on fawn survival. The spatial distribution and the range of predicted body masses were closely similar in males and females. The result of this study is therefore consistent with the view that the life history traits of roe deer are only weakly influenced by sexual selection. The occurrence of three plant species that are known to be important food items in spring/summer roe deer diets, hornbeam (Carpinus betulus), bluebell (Hyacinthoides sp.) and Star of Bethlehem (Ornithogalum sp.) was positively related to winter fawn body mass. The occurrence of species known to be avoided in spring/summer roe deer diets [e.g. butcher's broom (Ruscus aculeatus) and beech (Fagus sylvatica)], was negatively related to fawn body mass. We conclude that the spatial variation in the body mass of fawns in winter in this forest is as important as the temporal variation, and that the distribution of plant species that are actively selected during spring and summer is an important determinant of spatial variation in winter fawn body mass. The availability of these plants is therefore likely to be a key factor in the dynamics of roe deer populations.}, bibtype = {article}, author = {Pettorelli, N and Dray, Stéphane and Gaillard, J M and Chessel, D and Duncan, P and Illius, A and Guillon, N and Klein, F and Van Laere, G}, journal = {Oecologia}, keywords = {ACP,Geostatistique,Multivarié,Spatial} }
@article{ title = {Multivariate analysis of incomplete mapped data}, type = {article}, year = {2003}, pages = {411-422}, volume = {7}, id = {acc3adb5-edaf-3e18-8680-5f0cb4711239}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2003b}, source_type = {article}, short_title = {Multivariate analysis of incomplete mapped data}, private_publication = {false}, abstract = {Classical multivariate analyses are based on matrix algebra and enable the analysis of a table containing measurements of a set of variables for a set of sites. Incomplete mapped data consist of measurements of a set of variables recorded for the same geographical region but for different zonal systems and with only a partial sampling of this zone. This kind of data cannot be analysed with usual multivariate methods because there is no common system of sites for all variables. We propose a new approach using GIS technology and NIPALS, an iterative multivariate method, to analyse the spatial patterns of this kind of data. Moreover, an extension of our method is that it can be used for areal interpolation purposes. We illustrate the method in analysing data concerning the distribution of roe deer weights over several years in a reserve.}, bibtype = {article}, author = {Dray, Stéphane and Pettorelli, N and Chessel, D}, journal = {Transactions in GIS}, keywords = {Multivarié,PLS,Spatial} }
@article{ title = {Broad-scale biodiversity pattern of the endemic tree flora of the Western Ghats (India) using canonical correlation analysis of herbarium records}, type = {article}, year = {2003}, pages = {429-444}, volume = {26}, id = {8cb0cdb0-8355-340b-8c3f-f25078570c99}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Gimaret-Carpentier2003}, source_type = {article}, short_title = {Broad-scale biodiversity pattern of the endemic tr}, private_publication = {false}, abstract = {A crucial step in understanding the origin and maintenance of biological diversity is the assessment of its distribution over space and time and across environmental gradients. At the regional scale, two important attributes of species can be assessed that provide insight into speciation processes: species geographical and environmental ranges. The endemic tree flora of the Western Ghats is an interesting case for analyzing broad-scale biodiversity patterns because of the steep environmental gradients that characterize this tropical region of India. We analysed species geographical and environmental ranges by Canonical Correlation Analysis of point data from herbarium collections. We performed partial analyses to discriminate spatial and environmental correlates of species distribution, and evaluate the contribution of higher taxonomic ranks to these ranges. We identified different levels of organization in the distribution of endemism: 1) general features, such as the concentration of endemic species in the southern part of the Western Ghats, and the decrease in endemic species richness along the altitudinal and the dry season length gradients, and 2) patterns specific to genera or families, such as species niche separation along the environmental gradients. Our analyses enabled us to formulate hypotheses about the diversification of the endemic tree flora of the Western Ghats. They also confirm the value of Canonical Correlation Analysis as the suitable method for collection data analysis.}, bibtype = {article}, author = {Gimaret-Carpentier, C and Dray, Stéphane and Pascal, J.-.P.}, journal = {Ecography}, keywords = {AC,Atlas,Muséum,Partial,Spatial,Trend surface analysis} }
@article{ title = {Consistency between ordination techniques and diversity measurements: two alternative strategies for species occurrence data}, type = {article}, year = {2003}, pages = {242-251}, volume = {84}, id = {0141e66d-428c-3f83-b462-94ddc80686e3}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Pelissier2003}, source_type = {article}, short_title = {Consistency between ordination techniques and dive}, private_publication = {false}, abstract = {Both the ordination of taxonomic tables and the measurements of species diversity aim to capture the prominent features of the species composition of a community. However, interrelations between ordination techniques and diversity measurements are seldom explicated and are mainly ignored by many field ecologists. This paper starts from the notion of the species occurrence table, which provides a unifying formulation for different kinds of taxonomic data. Here it is demonstrated that alternative species weightings can be used to equate the total inertia of a centered-by-species occurrence table with common diversity indices, such as species richness, Simpson diversity, or Shannon information. Such an equation defines two main ordination strategies related to two different but consistent measures of species diversity. The first places emphasis on scarce species and is based on Correspondence Analysis and species richness (CA-richness strategy). The second, in which abundant species are prominent, relies on Non-Symmetric Correspondence Analysis and Simpson diversity (NSCA-Simpson strategy). Both strategies are suitable for measuring ? and ? diversity by analyzing the centered-by-species occurrence table with respect to external environmental or instrumental variables. In this paper, these two strategies are applied to ecological data obtained in a Neotropical rainforest plot. The results are then discussed with respect to the intrinsic characteristics of the community under analysis, and also to the broad classes of floro-faunistic data used in ecology (i.e., data gathered from museum or herbarium collections, exhaustive inventories in a reference plot, or enumeration through species-by-relevés tables). The approach encompasses several well-known techniques such as Correspondence Analysis, Non-Symmetric Correspondence Analysis, Canonical Correspondence Analysis, and Redundancy Analysis, and provides greater insight into interrelations between ordination methods and diversity studies.}, bibtype = {article}, author = {Pélissier, R and Couteron, P and Dray, Stéphane and Sabatier, D}, journal = {Ecology}, keywords = {AFC,ANSC,Diversité Beta,Ordination,forest} }
@phdthesis{ title = {Eléments d'interface entre analyses multivariées, systèmes d'information géographique et observations écologiques}, type = {phdthesis}, year = {2003}, city = {Lyon}, institution = {Université Lyon I}, id = {4e174964-9399-3711-b69f-761912f4b99e}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2003f}, source_type = {phdthesis}, short_title = {Eléments d'interface entre analyses multivariées,}, user_context = {Thèse de doctorat}, private_publication = {false}, bibtype = {phdthesis}, author = {Dray, Stéphane} }
@article{ title = {Within-plot relationships between tree species occurrences and hydrological soil constraints: an example in French Guiana investigated through canonical correlation analysis}, type = {article}, year = {2002}, pages = {143-156}, volume = {162}, id = {1a91fbea-0754-3ae0-a9ca-7f090ed12ef9}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Pelissier2002}, source_type = {article}, short_title = {Within-plot relationships between tree species occ}, private_publication = {false}, abstract = {Spatial relationships between tree species and hydrological soil constraints are analysed within a 10-ha rainforest plot at Piste de St Elie in French Guiana. We used canonical correlation analysis to cross directly the occurrence-by- species table of 4 992 individuals (d.b.h. > 10 cm) belonging to 120 species with qualitative soil variables and quantitative spatial data. Firstly, the list of species occurrences was confronted to nine soil descriptors characterising a weathering sequence from the initial well-drained ferralitic cover to transformed hydromorphic soil conditions. This analysis revealed that, apart from some specialised species restricted to the swamps that experience prolonged water saturation, the most abundant species can be ordered along two intermingled gradients of tolerance limiting their niche amplitude: a main gradient of tolerance to prolonged water saturation that appears down slope during the weathering sequence; a second gradient of less importance, displaying the species intolerant of prolonged water saturation according to their tolerance to temporary confinement of the uphill transformed soil systems due to the late appearance of a perched water-table. The results support the hypothesis that at Piste de St Elie, the constraining soil conditions imposed by surface water saturation are more important determinants for tree zonation of many tree species than water shortage. Secondly, the list of species occurrences was confronted to a spatial data table built from a trend surface regression of the tree coordinates. This analysis indicated that soil drainage is the main structuring factor of the local multispecies spatial pattern. After partialling out the soil effect, the multispecies pattern revealed a broader scale of heterogeneity that we supposed to be linked to endogenous factors resulting from population dynamics. Implications of the results are then discussed in the perspective of future research on tree zonation, local diversity pattern and community structuring in tropical rainforests.}, bibtype = {article}, author = {Pélissier, R and Dray, Stéphane and Sabatier, D}, journal = {Plant Ecology}, number = {2}, keywords = {AC,forest} }
@article{ title = {Matching data sets from two different spatial samples}, type = {article}, year = {2002}, pages = {867-874}, volume = {13}, id = {0bf3a629-7f11-3f93-91d4-1ee3c80cbe09}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2002}, source_type = {article}, short_title = {Matching data sets from two different spatial samp}, private_publication = {false}, abstract = {Methods for coupling two data sets (species composition and environmental variables for example) are well known and often used in ecology. All these methods require that variables of the two data sets have been recorded at the same sample stations. But if the two data sets arise from different sample schemes, sample locations can be different. In this case, scientists usually transform one data set to conform with the other one that is chosen as a reference. This inevitably leads to some loss of information. We propose a new ordination method, named spatial-RLQ analysis, for coupling two data sets with different spatial sample techniques. Spatial-RLQ analysis is an extension of co-inertia analysis and is based on neighbourhood graph theory and classical RLQ analysis. This analysis finds linear combinations of variables of the two data sets which maximize the spatial cross-covariance. This provides a co-ordination of the two data sets according to their spatial relationships. A vegetation study concerning the forest of Chizé (western France) is presented to illustrate the method.}, bibtype = {article}, author = {Dray, Stéphane and Pettorelli, N and Chessel, D}, journal = {Journal of Vegetation Science}, keywords = {Co-Inertie,Multivarié,RLQ,Spatial} }
@inproceedings{ title = {The distribution of preferred plant species in spring determines spatial variation in the body mass of roe deer fawns in winter}, type = {inproceedings}, year = {2002}, city = {Québec, Canada}, id = {6885ef7c-018e-335f-9589-18c12f6d6b51}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Pettorelli2002}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Pettorelli, N and Dray, Stéphane and Gaillard, J M and Chessel, D and Klein, F and Van Laere, G}, booktitle = {5th International Deer Biology Congress} }
@article{ title = {Modelling bovine trypanosomosis spatial distribution by GIS in an agro-pastoral zone of Burkina Faso}, type = {article}, year = {2002}, pages = {5-18}, volume = {56}, id = {10e7e2ca-5e7e-321a-a02b-014e3a212b37}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Michel2002}, source_type = {article}, short_title = {Modelling bovine trypanosomosis spatial distributi}, private_publication = {false}, abstract = {Modelling of the spatial distribution of bovine trypanosomosis prevalence in Sideradougou district Burkina Faso was performed by using a combination of spatial and statistical analysis. Based on a comprehensive and geographically representative census of herds and farms in the area, more than 2000 cattle were randomly chosen and their blood sampled during field survey. Data on livestock farming practices were recorded for each farm. All data were mapped within a GIS to generate new information on spatial constraints in the area. Surveys results were analysed and serological prevalence data were modelled using logistic regression. The model allowed identification and quantification of risk factors. In a second step the statistical model was used predictively on the entire farm population in the area. This method was successful in predicting the serological prevalence for each individual herd in the sample, from their livestock management patterns and spatial location. Predicted prevalences were represented within the GIS, taking daily movements of animals into account. Spatial distribution of prevalence would illustrate specific locations at risk from an epidemiological viewpoint. It gives evidence that the hydrological network and land occupation patterns in the savanna-type countryside are playing an important part when structuring a so-called "trypanosomosis space".}, bibtype = {article}, author = {Michel, J F and Dray, Stéphane and de La Rocque, S and Desquesnes, M and Solano, P and De Wispelaere, G and Cuisance, D}, journal = {Preventive Veterinary Medicine}, keywords = {Epidemiologie,GLM,Geostatistique,SIG,Spatial} }
@inproceedings{ title = {Systèmes d'information géographique : une application à la modélisation d'une maladie à transmission vectorielle au Burkina Faso}, type = {inproceedings}, year = {2001}, city = {Lyon, France}, id = {14325e50-3ef2-3dfa-aafb-e473a5c260ab}, created = {2010-11-03T21:13:25.000Z}, file_attached = {false}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray2001}, notes = {Seminar}, private_publication = {false}, bibtype = {inproceedings}, author = {Dray, Stéphane}, booktitle = {Séminaire de l'UMR 5558, 29 November} }
@inproceedings{ title = {Modelling bovine trypanosomosis spatial distribution by GIS in an agro-pastoral zone of Burkina Faso}, type = {inproceedings}, year = {2001}, city = {Lancaster University, England}, id = {287f3dd4-c744-3e7a-a462-58f3b5e48604}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Michel2001}, source_type = {inproceedings}, notes = {Conference}, private_publication = {false}, bibtype = {inproceedings}, author = {Michel, J F and Dray, Stéphane and de La Rocque, S and Desquesnes, M and Solano, P and De Wispelaere, G and Cuisance, D}, booktitle = {GISVET Conference}, keywords = {Multivarié,Spatial} }
@phdthesis{ title = {Utilisation des listes d'occurrences spécifiques spatialisées en écologie et biogéographie}, type = {phdthesis}, year = {1999}, city = {Lyon}, institution = {Université Lyon I}, id = {9f6cc12a-ceb7-3f8a-866b-8e542cf48109}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray1999a}, source_type = {phdthesis}, short_title = {Utilisation des listes d'occurrences spécifiques s}, user_context = {Rapport bibliographique, DEA Analyse et Modélisation des Systèmes Biologiques}, private_publication = {false}, bibtype = {phdthesis}, author = {Dray, Stéphane}, keywords = {AC,ACC} }
@phdthesis{ title = {L'ordination des listes d'occurrences : quand l'analyse canonique des correspondances est une analyse canonique}, type = {phdthesis}, year = {1999}, city = {Lyon}, institution = {Université Lyon I}, id = {4b069dd0-96c0-3d37-bdf1-587737d6f28e}, created = {2010-11-03T21:13:25.000Z}, file_attached = {true}, profile_id = {976aa121-3316-304c-8340-7ca54d70abe6}, last_modified = {2017-03-16T14:38:37.564Z}, read = {true}, starred = {false}, authored = {true}, confirmed = {true}, hidden = {false}, citation_key = {Dray1999}, source_type = {phdthesis}, short_title = {L'ordination des listes d'occurrences : quand l'an}, user_context = {Rapport technique, DEA Analyse et Modélisation des Systèmes Biologiques}, private_publication = {false}, bibtype = {phdthesis}, author = {Dray, Stéphane}, keywords = {AC,ACC} }