Mots-clés

Publications (dernière mise à jour le 22 septembre 2009)

Livre

• King, R., Morgan, B.J.T., Gimenez, O. and S.P. Brooks (2009). Bayesian Analysis for Population Ecology. CRC Press. http://lemur.mcs.st-and.ac.uk/Book-website/
   

Articles

In press

• Gimenez, O. and R. Choquet (in press). Incorporating individual heterogeneity in studies on marked animals using numerical integration: capture-recapture mixed models. Ecology.

• Cubaynes, S. Pradel, R. Choquet, R. Duchamp, C. Gaillard, J.-M., Lebreton, J.-D., Marboutin, E., Miquel, C., Reboulet, A.-M., Poillot, C., Taberlet, P. and O. Gimenez. (in press). Importance of accounting for detection heterogeneity when estimating abundance: the case of French wolves. Conservation Biology.

• Abadi, F., Gimenez, O., Arlettaz, R. and M. Schaub (in press). A simulation assessment of integrated population models: bias, accuracy, and violation of the assumption of independence. Ecology.

• Abadi, F., Gimenez, O., Ullrich, B., Arlettaz, R. and M. Schaub (in press). Estimation of immigration rate using integrated population models. Journal of Applied Ecology.

• Besnard, A., Novoa, C. and O. Gimenez. (in press). Hunting impact on Pyrenean gray partridge population dynamics. Wildlife Biology.

• Péron, G., Crochet, P.A.C., Choquet, R., Pradel, R., Lebreton, J.-D. and O. Gimenez. (in press) Heterogeneity capture-recapture models to study survival senescence in the wild. Oïkos.

• Mihoub, J.-B., Gimenez, O., Pilard, P. and F. Sarrazin (in press). Challenging conservation of migratory species: Sahelian rainfalls drive first-year survival of the vulnerable Lesser Kestrel Falco naumanni. Biological Conservation.

2009

• Gimenez, O., Grégoire, A. and T. Lenormand (2009). Estimating and visualizing fitness surfaces using mark-recapture data. Evolution. 63:3097–3105

• Choquet, R., Lebreton, J.-D., Gimenez, O., Reboulet, A.-M., and R. Pradel. (2009). U-CARE: Utilities for performing goodness of fit tests and manipulating CApture-REcapture data. Ecography. 32: 1071-1074

• Kazakou, E., Violle, C, Roumet, C., Pintor, C., Gimenez, O. and E. Garnier. (2009). Litter quality and decomposability of species from a Mediterranean succession depend on leaf traits but not on nitrogen supply. Annals of Botany. 104:1151-1161

• Grosbois, V., Harris, M. P., Anker-Nilssen, T., McCleery, R. H., Shaw, D. N., Morgan, B.J.T. and O. Gimenez (2009). Modeling survival at multi-population scales using mark–recapture data. Ecology.90:2922–2932

• Guilhaumon, F. O. Gimenez, K. J. Gaston, and D. Mouillot (2008). Reply to Bode and Murdoch: A proper integration of species-area relationship uncertainties into return on investment analyses is needed. Proceedings of the National Academy of Sciences. 106:E13

• Bischof, R. J. E. Swenson, N. G. Yoccoz, A. Mysterud, and O. Gimenez (2009). The demographic pattern of seasonally varying cause-specific vulnerability in hunted brown bears: competing risk survival and multistate mark-recapture analysis. Journal of Animal Ecology. 78:656–665

• Mennerat, A., P. Perret, P. Bourgault, J. Blondel, O. Gimenez, D. W. Thomas, P. Heeb, M. M. Lambrechts (2009). Aromatic plants in nests of blue tits: positive effects on nestlings. Animal Behaviour. 77: 569–574  

• Gimenez, O., S. Bonner, R. King, R. A. Parker, S.P. Brooks, L. E. Jamieson, V. Grosbois, B. J. T. Morgan, and L. Thomas (2009). WinBUGS for Population Ecologists: Bayesian Modeling Using Markov Chain Monte Carlo Methods. In Modeling Demographic Processes in Marked Populations. Thomson, D. L.; Cooch, E. G.; Conroy, M. J. (Eds.). Springer Series: Environmental and Ecological Statistics, Vol. 3, pages 883-915. . Code available here.

• Gimenez, O., Morgan, B.J.T. and S.P. Brooks (2009). Weak Identifiability in Models for Mark-Recapture-Recovery Data. In Modeling Demographic Processes in Marked Populations. Thomson, D. L.; Cooch, E. G.; Conroy, M. J. (Eds.). Springer Series: Environmental and Ecological Statistics, Vol. 3, pages 1055-1067. . R & WinBUGS codes.

• Gimenez, O. and C. Barbraud (2009). The Efficient Semiparametric Regression Modeling of CaptureRecapture Data: Assessing the Impact of Climate on Survival of Two Antarctic Seabird Species. In Modeling Demographic Processes in Marked Populations. Thomson, D. L.; Cooch, E. G.; Conroy, M. J. (Eds.). Springer Series: Environmental and Ecological Statistics, Vol. 3, pages 43-58.

• Borysiewicz, R.S., B.J.T. Morgan, V. Hénaux, T. Bregnballe, J-D. Lebreton, and O. Gimenez (2009). An Integrated Analysis of Multisite Recruitment, Mark-Recapture- Recovery and Multisite Census Data. In Modeling Demographic Processes in Marked Populations. Thomson, D. L.; Cooch, E. G.; Conroy, M. J. (Eds.). Springer Series: Environmental and Ecological Statistics, Vol. 3, pages 579-591.

2008

• Guilhaumon, F. O. Gimenez, K. J. Gaston, and D. Mouillot (2008). Taxonomic & regional uncertainty in species-area relationships and the identification of richness hotspots. Proceedings of the National Academy of Sciences. 105:15458–15463 , supplementary information .

• Gimenez, O., A. Viallefont, A. Charmantier, R. Pradel, E. Cam, C. R. Brown, M. D. Anderson, M. Bomberger Brown, R. Covas, J.-M. Gaillard (2008). The risk of flawed inference in evolutionary studies when detectability is less than one. The American Naturalist. 172:441–448. 

• Gimenez, O. (2008). Discussion: Towards a Bayesian analysis template? The Canadian Journal of Statistics. 36: 21-24.  

• Grosbois V., Gimenez O., Gaillard, J.-M., Pradel, R., Barbraud, C., Clobert, J., Møller, A. P. and H. Weimerskirch (2008). Assessing the impact of climate variation on survival in vertebrate populations. Biological Reviews. 83:357-399.

• Pradel, R., L. Maurin-Bernier, O. Gimenez, M. Genovart, R. Choquet, and D. Oro. Estimation of sex-specific survival with uncertainty in sex assessment (2008). The Canadian Journal of Statistics. 36: 29-42.  

• Charpentier, M.J.E., F. Prugnolle, O. Gimenez and A. Widdig. Genetic variation and sociality in a primate species (2008). Behavior Genetics. 38: 151-158.

• Ghimire, S., Gimenez, O., Pradel, R., McKey, D., and Y. Aumeeruddy-Thomas (2008). Demographic variation and population viability in a threatened Himalayan medicinal and aromatic herb (Nardostachys grandiflora): matrix modelling of harvesting effects in two contrasting habitats. Journal of Applied Ecology. 45: 41-51.

2007

• Véran, S., Gimenez, O., Flint, E., Kendall, B., Doherty, P., and J.-D. Lebreton (2007). Quantifying the impact of longline fisheries on adult survival in the Black-footed Albatross. Journal of Applied Ecology. 44: 942–952.

• Gimenez, O., V. Rossi, R. Choquet, C. Dehais, B. Doris, H. Varella, J.-P. Vila and R. Pradel (2007). State-space modelling of data on marked individuals. Ecological Modelling. 206: 431-438.

• Schaub, M., Gimenez, O., Sierro, A. and R. Arlettaz (2007). Use of Integrated Modeling to Enhance Estimates of Population Dynamics Obtained from Limited Data. Conservation Biology. 21: 945–955.

• Kazakou, E., E. Garnier and Gimenez, O. (2007). Assessing the relative contribution of leaf lifespan and nutrient resorption to mean residence time: an elasticity analysis. Ecology. 88: 1857-1863.

• Pinay, G., B. Gumiero, E. Tabacchi, O. Gimenez, A.M. Tabacchi-Planty, M.M. Hefting, T.P. Burt, V.A. Black, C. Nilsson, V. Iordache, F. Bureau, L. Vought, G.E. Petts and H. Décamps. (2007). Patterns of denitrification rates in European alluvial soils under various hydrological regimes. Freshwater Biology. 52: 252–266.

2006

• Gimenez O., C. Crainiceanu, C. Barbraud, S. Jenouvrier and B.J.T. Morgan. (2006). Semiparametric regression in capture-recapture modelling. Biometrics. 62: 691-698. - R & WinBUGS codes

• Gimenez, O., R. Covas, C. R. Brown, M. D. Anderson, M. Bomberger Brown and T. Lenormand. (2006). Nonparametric estimation of natural selection on a quantitative trait using mark-recapture data. Evolution. 60: 460-466. - R & WinBUGS codes

2005

• Charpentier M., Peignot P., Hossaert-McKey M., Gimenez O., Setchell J. and E.J. Wickings (2005). Constraints on control: factors influencing reproductive success in male mandrils (Mandrillus sphinx). Behavioral Ecology. 16: 614-623.

• Do F.C., Goudiaby V.A., Gimenez O., Diagne A.L., Diouf M., Rocheteau A., Akpo L.E. (2005) Environmental influence on canopy phenology in the dry tropics. Forest Ecology and Management. 215: 319-328.

• Gimenez O., Choquet R., Lamor L., Scofield P., Fletcher D., J.-D. Lebreton and R. Pradel (2005). Efficient Profile-Likelihood Confidence Intervals for Capture-Recapture Models. Journal of Agricultural, Biological, and Environmental Statistics 10: 184-196. - M-SURGE

• Pradel, R., Gimenez O. and J.-D. Lebreton (2005). Principles and interest of GOF tests for multistate capture-recapture models. Animal Biodiversity and Conservation 28: 189–204. -

• Ancrenaz M., Gimenez O., Ambu L., Ancrenaz K., Andau P., Goossens B., Payne J., Tuuga A. and I. Lackman- Ancrenaz (2005). Aerial Survey Gives New Estimates for Orang-utans in Sabah, Malaysia. Plos Biology 3: 30-37.

2004

• Gimenez O., Viallefont A., Choquet R., Catchpole E.A. and B.J.T. Morgan (2004). Methods for investigating parameter redundancy. Animal Biodiversity and Conservation 27: 561-572.

• Choquet R., Reboulet A.-M., Pradel R., Gimenez O. and J.-D. Lebreton (2004). M-SURGE : new software specically designed for multistate capture-recapture models. Animal Biodiversity and Conservation 27: 207-215. -

• Schaub M., Gimenez O., Schmidt B.R. and R. Pradel (2004). Estimating survival and temporary emigration in the multistate capture-recapture framework. Ecology 85: 2107-2113. - Maple and Matlab codes

• Ancrenaz M., Goossens B., Gimenez O., Sawang A. and I. Lackman-Ancrenaz (2004). Determination of ape distribution and population size using ground and aerial surveys : a case study with orang-utans in lower Kinabatangan, Sabah, Malaysia. Animal Conservation 7: 375-385.

• Charpentier M., Hossaert-McKey M., Peignot P., Gimenez O., Setchell J.M. and E.J. Wickings (2004). Social factors and male reproductive success in a highly sexually dimorphic primate: Paternity analysis over a 20 year period in a group of mandrills (Mandrillus sphinx). Folia Primatologica 75 (supp. 1):244-245.

2003

• Gimenez O., Choquet R. and J.-D. Lebreton (2003). Parameter redundancy in multistate capture-recapture models. Biometrical Journal 45: 704-722. - Maple code

• Pradel R., Wintrebert C.M.A. and Gimenez O. (2003). A proposal for a goodness-of-fit test to the Arnason-Schwarz multisite capture-recapture model. Biometrics 59: 43-53.

• Besnard A., Gimenez O. et J.-D. Lebreton (2002). A model for the evolution of creching behaviour in gulls. Evolutionary Ecology 16: 489-503.

Post-docs

• 2008-2010 (2 years): Population dynamics of exploited populations: Wild board as a case study, Sabrina Servanty.

• 2009-2010 (1 year): Environmental variation and population dynamics of bats, Elena Papadatou (with R. Pradel).

• 2006 (3 months): Estimating juvenile survival of Emperor penguins using integrated population modelling, Sophie Véran (with C. Barbraud). Present position: Post-doct Patuxent

PhD students

• 2009-2011: Capture-recapture mixed models, Sarah Cubaynes, Biostatistics (with C. Lavergne).

• 2009-2011: Evolutionary ecology in the wild using mark-recapture data: Atlantic salmons (Salmo salar) as a case study, Mathieu Buoro, Biologie (with E. Prévost).

• 2008-2010: Analysis of biodiversity patterns at large scale and conservation biogeography: methodological insights, François Guilhaumon, Biology (with D. Mouillot).

Masters

• 2009: PLS analysis of capture-recapture data, Soad Bouhazama, stage M2 Recherche Biostatistique.

• 2009: Predictors of extinction risks in fragmented population, Amel Berrima, stage M2 Recherche Conservation de la BioDiversité (with K. Theodorou).

• 2009: Population dynamics of exploited species: the case study of Red-legged Partridge Alectoris rufa, Marlène Gamelon, stage M1 BEE.

• 2008: Heritability of demographic parameters using mark-recapture data, Julien Papaïx, stage M2 Recherche Biostatistique.

• 2008: Impact of climatic conditions on Black grouse (Tetrao tetrix) reproduction in the Alps, Jean-Yves Barnagaud (with P.-A. Crochet).

• 2008 : Life-history tradeoffs in juveniles of the Atlantique salmons (Salmo salar) using mark-recapture data, Mathieu Buoro (with E. Prévost), stage M2 Recherche BEE.

• 2008 : Estimating abundance of wolves (Canis lupus) in the French Alps: importance of detection heterogeneity, Sarah Cubaynes (with J.-M. Gaillard), stage M2 Recherche Lyon.

• 2008 : Spatial Modeling of Bird Densities in Scotland: Accounting for Detectability Less Than One, Saqlain Raza, stage M2 Recherche Biostatistique.

• 2007: Integrating path analyses in mark-recapture models: cost of reproduction on blue tits survival, Sarah Cubaynes, stage M1 BGAE option BioStat, CEFE (with C. Doutrelant, V. Grosbois & P. Perret).

• 2007: "Estimating selection gradients on morphological traits in common blackbirds using mark-recapture data", Dounia Saleh, stage M1 BGAE option EBE, CEFE (with A. Grégoire).

• 2007: "Ecological and morphological factors affecting olfaction in procellariiforms", Paul Bacquet, stage M1 BGAE option EBE, CEFE (with F. Bonadonna).

• 2007: "Bayesian model selection for integrated population models", Marie Cheminat, stage M2 Recherche Biostatistique, INRA/CEFE (with J.-P. Vila).

• 2005: "Integrated population modelling for population dynamics: applications of particle filtering algorithms", Blaise Doris, DEA BioStatistique, Université de Montpellier II (with V. Rossi).

• 2004: "Hidden-Markov models for capture-recapture data", Lauriane Rouan, DEA BioStatistique, Université de Montpellier II  (with R. Pradel).

• 2004: "A Bootstrapped goodness-of-fit test for mixture of multinomials with applications to capture-recapture data", Thomas Filleron, DEA BioStatistique, Université de Montpellier II  (with R. Pradel).

• 2004: "Statistical Inference in Species Area Curves", Francois Guilhaumon, DEA BioStatistique, Université de Montpellier II  (with D. Mouillot).

• 2003: "Parameter-redundancy in multievent capture-recapture models", Lory Maurin, DEA BioStatistique, Université de Montpellier II (with R. Pradel).

• 2002: "Profile-likelihood confidence intervals for multistate capture-recapture models", Laurent Lamor, DEA BioStatistique, Université de Montpellier II (with R. Pradel).

Engineers

• 2006: "Incorporating covariates in distance sampling models in a Bayesian framework", Jérémy Piffady, stage pré-doctoral en BioStatistique, University of StAndrews (with S.T. Buckland).

• 2004: "Software and Integrated Population Modelling for plants", Grégoire Michau, École Polytechnique, Université de Grenoble (with F. Nicole).

• 2004: "Handling heaping in distance sampling models", Bouaynaya Samed & Bouzoubaa Mohamed, ENSIMAG, Université de Grenoble.

Enseignements

ateliers de travail

• Cours et TDs "Workshop CR 2009 – Modelling individual histories with state uncertainty". 16-20 Novembre 2009, Montpellier, France.

• Cours et TDs "Bayesian Methods for Population Ecology". 7-10 Septembre 2009, StAndrews, UK.

• Cours et TDs "Workshop CR 2008 – Modelling individual histories with state uncertainty". 17-21 Novembre 2008, Montpellier, France.

• Cours et TDs "Workshop CR 2007 – Quantitative Methods in Population Dynamics". 11-15 June 2007, Mytilene, Greece.  

• Cours et TDs "Workshop CR 2006 – Analysis of multistate capture-recapture data: modelling incomplete individual histories". 14-17 Novembre 2006, Patuxent Wildlife Research Center, Laurel, USA.

• Cours et TDs "Bayesian Methods for Population Ecology" 4-8 Septembre 2005, Cambridge, GB.

• TDs "Workshop CR 2005 – Analysis of multistate capture-recapture data: modelling incomplete individual histories". 19-23 Septembre 2005, Montpellier, France.

• Cours et TDs "Statistics in practice using SPSS" et "Counting animals with Distance sampling methods using Distance 3.5". Kota-Kinabalu (Sabah) Malaisie. Juillet 2003.

• Cours et TDs "Analysis of Multistate Capture-Recapture Data: Modelling Incomplete Individual Histories". Workshop.  Montpellier. Mars 2003.

• Cours et TDs "Analysis of Multistate Capture-Recapture Data: Modelling Incomplete Individual Histories". Workshop.  Montpellier. Mars 2002.

• TDs "Qualitative statistical data analysis and generalized linear model" organisé par le CEFE/CNRS pour l'Office National de la Chasse et de la Faune Sauvage (ONCFS).