Mark-Recapture with state uncertainty

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Mark-Recapture with state uncertainty

Postby rplp » Mon Oct 19, 2015 10:58 am

Upcoming workshop on the analysis of capture-recapture data using multievent models to be held at Center for Evolutionary and Functional Ecology (CEFE), Montpellier, France, 21-25 March 2016. The registration of participants will be at CEFE the 21 March on evening and will be followed by 3 days of lectures and practical exercises plus 1 day of practical work on the participants' data.

You are hereby cordially invited to take part in the following workshop:

MODELLING INDIVIDUAL HISTORIES WITH STATE UNCERTAINTY

organized by the Biostatistics and Population Biology team of CEFE in Montpellier (France)

The estimation of population parameters (survival, recruitment, dispersal, and population growth rate) is critical to many areas of fundamental and applied biology. The major source of data for such estimation comes from observations of marked animals. This workshop will deal with recent advances in the analysis of such data. The content is aimed at providing the participants with a solid background in the philosophy, theory and practices for the analysis of data from marked animals, with a specific focus on multievent data and models. Multievent capture-recapture models are a natural generalization of the multisite recapture models. Similarly, individuals are sampled on discrete occasions, at which they may be captured or not. However, contrary to the multisite case, uncertainty in the assessment of state such as breeder, diseased or highly catchable can be incorporated into the analysis. Conceptually, it is not states that are observed but rather something dubbed an "event" (a particular breeding behaviour, a positive blood test or just encounter), which reflects to some extent the underlying state. The presence of imperfect observations and the lack of information on individual quality presently make multievent models an invaluable tool in virtually any area of population biology. Current applications include the study of dispersal, epidemiology, individual heterogeneity, mixture of information... New developments allow the treatment of individual heterogeneity through random effects as well as through mixture models, and the inclusion of individual as well as environmental covariates. For examples of topics that can be addressed in the multievent framework, see the non-exhaustive bibliography below. Depending on the majority of participants wishes, one of the following theme will be developped during the workshop:
  • stopover
  • epidemiology
  • site occupancy


Emphasis will be placed on stringent procedures for building and selecting the most appropriate models for the data set at hand, in order to be able to draw reliable biological conclusions.

Format of the workshop will be a combination of lectures and computer lab exercises with the programs E-SURGE and U-CARE. (http://www.cefe.cnrs.fr/fr/recherche/bc/bbp/1045-desc/264-logiciels). U-CARE incorporates goodness-of-fit tests for multistate models, and E-SURGE makes the building of complex models easy based on a language describing the structure of models in a compact and user-friendly way. All lectures and course material will be in English.

It is our hope that participants will bring their own capture-recapture data to work on them during the workshop. To take full advantage of the workshop, it is expected that the participants will have some basic practice of the analysis of CR data.

Teachers: Roger Pradel, Rémi Choquet, Olivier Gimenez, Tamar Lok, and Emmanuelle Cam.

Participants will have to provide their own laptop computer that is capable of running Windows-based software.

Thank you for disseminating this message to colleagues and students who may not have received it.

The workshop organizers
Roger Pradel, Rémi Choquet, Olivier Gimenez

For application, go to http://multievent.sciencesconf.org/

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Dispersal:
Avril A, Letty J, Pradel R, Léonard Y, Santin-Janin H, Pontier D (2012). A multi-event model to study stage-dependence dispersal in radio-collared hares: when hunting promotes costly transience. Ecology 93:1305-1316.
Balkız Ö, Béchet A, Rouan L, Choquet R, Germain C, Aguilar Amat J, Rendón-Martos M, Baccetti N, Nissardi S, Özesmi U, Pradel R (2010) Experience-dependent natal philopatry of breeding Greater flamingos. Journal of Animal Ecology 79:1045-1056.
Devillard, S. and Y. Bray (2009). Assessing the effect on survival of natal dispersal using multistate capture-recapture models. Ecology 90(10): 2902-2912.
Doxa A, Besnard A, Bechet A, Pin C, Lebreton JD, Sadoul N (2013) Inferring dispersal dynamics from local population demographic modelling: the case of the slender-billed gull in France. Animal Conservation 16:684-693
Gauthier G, Milot E, Weimerskirch H (2012). Estimating dispersal, recruitment and survival in a biennially breeding species, the Wandering Albatross. Journal of Ornithology 152:S457-S467. 10.1007/s10336-010-0541-9

Epidemiology:
Chambert T, Staszewski V, Lobato E, Choquet R, Carrie C, McCoy KD, Tveraa T, Boulinier T (2012). Exposure of black-legged kittiwakes to Lyme disease spirochetes: dynamics of the immune status of adult hosts and effects on their survival. Journal of Animal Ecology 81:986-995. 10.1111/j.1365-2656.2012.01979.x
Conn, P. B. and E. G. Cooch (2009). Multistate capture-recapture analysis under imperfect state observation: an application to disease models. Journal of Applied Ecology 46(2): 486-492.
Cooch EG, Conn PB, Ellner SP, Dobson AP, Pollock KH (2009). Disease dynamics in wild populations: modeling and estimation: a review. Journal of Ornithology 152:S485-S509. 10.1007/s10336-010-0636-3
Lachish S, Knowles SCL, Alves R, Wood MJ, Sheldon BC (2011). Infection dynamics of endemic malaria in a wild bird population: parasite species-dependent drivers of spatial and temporal variation in transmission rates. Journal of Animal Ecology 80:1207-1216. 10.1111/j.1365-2656.2011.01893.x

Individual heterogeneity:
Cam E, Gimenez O, Alpizar-Jara R, Aubry LM, Authier M, Cooch EG, Koons DN, Link WA, Monnat J-Y, Nichols JD, Rotella JJ, Royle JA, Pradel R (2013). Looking for a needle in a haystack: inference about individual fitness components in a heterogeneous population. Oikos. 122: 739-753.
Crespin, L., R. Choquet, et al. (2008). "Is heterogeneity of catchability in capture-recapture studies a mere sampling artifact or a biologically relevant feature of the population?" Population Ecology 50(3): 247-256.
Cubaynes S, Lavergne C, Marboutin E, Gimenez O (2012). Assessing individual heterogeneity using model selection criteria: how many mixture components in capture-recapture models? Methods in Ecology and Evolution 3:564-573. 10.1111/j.2041-210X.2011.00175.x
Cubaynes, S., R. Pradel, et al. (2010). "Importance of Accounting for Detection Heterogeneity When Estimating Abundance: the Case of French Wolves." Conservation Biology 24(2): 621-626.
Fletcher D, Lebreton JD, Marescot L, Schaub M, Gimenez O, Dawson S, Slooten E (2012). Bias in estimation of adult survival and asymptotic population growth rate caused by undetected capture heterogeneity. Methods in Ecology and Evolution 3:206-216. 10.1111/j.2041-210X.2011.00137.x
Gimenez, O. and R. Choquet (2010). "Individual heterogeneity in studies on marked animals using numerical integration: capture-recapture mixed models." Ecology 91(4): 951-957.
Gourlay Larour M-L, Pradel R, Guillemain M, Santin-Janin H, L'Hostis M, Caizergues A (2013) Individual turnover in Common Pochards wintering in western France. Journal of Wildlife Management: 77(3): 477-485.
Marescot L, Pradel R, Duchamp C, Cubaynes S, Marboutin E, Choquet R, Miquel C, Gimenez O (2011) Capture-recapture population growth rate as a robust tool against detection heterogeneity for population management. Ecological Applications 21:2898-2907.
Marzolin G, Charmantier A, Gimenez O (2011). Frailty in state-space models: application to actuarial senescence in the Dipper. Ecology 92:562-567. 10.1890/10-0306.1
Oliver LJ, Morgan BJT, Durant SM, Pettorelli N (2011). Individual heterogeneity in recapture probability and survival estimates in cheetah. Ecological Modelling 222:776-784. 10.1016/j.ecolmodel.2010.11.021
Peron, G., P. A. Crochet, et al. (2010). "Capture-recapture models with heterogeneity to study survival senescence in the wild." Oikos 119(3): 524-532.
Peron, G., J. D. Lebreton, et al. (2009). "Breeding dispersal in black-headed gull: the value of familiarity in a contrasted environment." Journal of Animal Ecology 79(2): 317-326.
Pradel R, Choquet R, Lima MA, Merritt JF, Crespin L (2010) Estimating population growth rate from capture-recapture data in presence of capture heterogeneity. Journal of Agricultural, Biological and Environmental Statistics 15:248-258. 10.1007/s13253-009-0008-8
Pradel R, Sanz-Aguilar A (2012) Modeling Trap-Awareness and Related Phenomena in Capture-Recapture Studies. PLOS One 7:e32666.
Veran, S., O. Gimenez, et al. (2007). "Quantifying the impact of longline fisheries on adult survival in the black-footed albatross." Journal of Applied Ecology 44(5): 942-952.
Mixture of information:
Duriez, O., S. A. Saether, et al. (2009). "Estimating survival and movements using both live and dead recoveries: a case study of oystercatchers confronted with habitat change." Journal of Applied Ecology 46(1): 144-153.
Gauthier, G. and J. D. Lebreton (2008). "Analysis of band-recovery data in a multistate capture-recapture framework." Canadian Journal of Statistics-Revue Canadienne De Statistique 36(1): 59-73.
Hardouin LA, Nevoux M, Robert A, Gimenez O, Lacroix F, Hingrat Y (2012). Determinants and costs of natal dispersal in a lekking species. Oikos 121:804-812. 10.1111/j.1600-0706.2012.20313.x
Juillet C, Choquet R, Gauthier G, Pradel R (2011) A capture-recapture model with double-marking, live and dead encounters, and heterogeneity of reporting due to auxiliary mark loss. Journal of Agricultural, Biological and Environmental Statistics 16:88-104.
Péron G, Ferrand Y, Choquet R, Pradel R, Gossmann F, Bastat C, Guénézan M, Bauthian I, Julliard R, Gimenez O (2012) Spatial heterogeneity in mortality and its impact on the population dynamics of Eurasian woodcocks. Population Ecology 54:305-312. 10.1007/s10144-012-0309-6
Sanz-Aguilar A, Tavecchia G, Genovart M, Igual JM, Oro D, Rouan L, Pradel R (2011) Studying the reproductive skipping behavior in long-lived birds by adding nest-inspection to individual-based data. Ecological Applications 21:555-564.
Recruitment and breeding probability:
Desprez M, Pradel R, Cam E, Monnat J-Y, Gimenez O (2011) Now you see him, now you don't: experience, not age, is related to reproduction in kittiwakes. Proceedings of the Royal Society of London Series B-Biological Sciences 278:3060-3066.
Hernández-Matías, A., J. Real, et al. (2010). "Determinants of territorial recruitment in Bonelli’s eagle (Aquila fasciata) populations." Auk 127(1): 173-184.
Juillet C, Choquet R, Gauthier G, Lefebvre J, Pradel R (2012) Carry-over effects of spring hunt and climate on recruitment to the natal colony in a migratory species. Journal of Applied Ecology: 49: 1237-1246. 10.1111/j.1365-2664.2012.02199.x
Lescroel, A., K. M. Dugger, et al. (2009). "Effects of individual quality, reproductive success and environmental variability on survival of a long-lived seabird." Journal of Animal Ecology 78(4): 798-806.
Lorentzen E, Choquet R, Steen H (2012). Modelling state uncertainty with photo series data for the estimation of breeding success in a cliff-nesting seabird. Journal of Ornithology 152:S477-S483. 10.1007/s10336-011-0723-0
Millon, A., S. J. Petty, et al. (2010). "Pulsed resources affect the timing of first breeding and lifetime reproductive success of tawny owls." Journal of Animal Ecology 79(2): 426-435.
Pradel R, Choquet R, Béchet A (2012) Breeding experience might be a major determinant of breeding probability in long-lived species: the case of the greater flamingo. PLOS One 7(12): e51016.
Reed, E. T., G. Gauthier, et al. (2005). "Effects of neck bands on reproduction and survival of female greater snow geese." Journal of Wildlife Management 69(1): 91-100.
Sanz-Aguilar, A., G. Tavecchia, et al. (2008). "The cost of reproduction and experience-dependent vital rates in a small petrel." Ecology 89(11): 3195–3203.
Schmaltz L, Cezilly F, Bechet A (2011). Using multistate recapture modelling to assess age-specific bottlenecks in breeding success: a case study in the greater flamingo Phoenicopterus roseus. Journal of Avian Biology 42:178-186. 10.1111/j.1600-048X.2010.05112.x
Tavecchia, G., R. Pradel, et al. (2007). "Density-dependent parameters and demographic equilibrium in open populations." Oikos 116(9): 1481-92.
Sources of mortality:
Schaub, M. and R. Pradel (2004). "Assessing the relative importance of different sources of mortality from recoveries of marked animals." Ecology 85(4): 930-8.
Tavecchia G, Adrover J, Muñoz Navarro A, Pradel R (2012) Modelling mortality causes in longitudinal data in the presence of tag loss: application to raptor poisoning and electrocution. Journal of Applied Ecology 49:297-305.
Sex or species uncertainty:
Genovart M, Pradel R, Oro D (2012) Exploiting uncertain ecological fieldwork data with multi-event capture-recapture modelling: an example with bird sex assignment. Journal of Animal Ecology 81:970-977. 10.1111/j.1365-2656.2012.01991.x
Hardouin LA, Nevoux M, Robert A, Gimenez O, Lacroix F, Hingrat Y (2012). Determinants and costs of natal dispersal in a lekking species. Oikos 121:804-812. 10.1111/j.1600-0706.2012.20313.x
Pradel, R., L. Maurin-Bernier, et al. (2008). "Estimation of sex-specific survival with uncertainty in sex assessment." Canadian Journal of Statistics-Revue Canadienne De Statistique 36(1): 29-42.
Runge, J. P., J. E. Hines, et al. (2007). "Estimating species-specific survival and movement when species identification is uncertain." Ecology 88(2): 282-288.
Stopover duration:
Choquet R, Guédon Y, Besnard A, Guillemain M, Pradel R (2013) Estimating Stop over Duration in presence of trap-effects. Ecological Modelling 250: 111-118.
Rivalan, P., R. Pradel, et al. (2006). "Estimating clutch frequency in the sea turtle Dermochelys coriacea using stopover duration." Marine Ecology-Progress Series 317: 285-295.
Verkuil, Y. I., J. J. Wijmenga, et al. (2010). "Spring migration of Ruffs Philomachus pugnax in Fryslan: estimates of staging duration using resighting data." Ardea 98(1): 21-33.
Trade-offs:
Rivalan, P., A.-C. Prévot-Julliard, et al. (2005). "Trade-off between current reproductive effort and delay to next reproduction in the leatherback sea turtle." Oecologia 145(4): 564-74.
Schaub, M. and J. von Hirschheydt (2009). "Effect of current reproduction on apparent survival, breeding dispersal, and future reproduction in barn swallows assessed by multistate capture-recapture models." Journal of Animal Ecology 78(3): 625-635.
Memory models:
Rouan, L., R. Choquet, et al. (2009). "A General Framework for Modeling Memory in Capture-Recapture Data." Journal of Agricultural Biological and Environmental Statistics 14(3): 338-355.
Migration:
Genovart M, Sanz-Aguilar A, Fernandez-Chacon A, Igual JM, Pradel R, Forero MG, Oro D (2013) Contrasting effects of climatic variability on the demography of a trans-equatorial migratory seabird. Journal of Animal Ecology 82: 121-130.
Lok T, Overdijk O, Piersma T. (2015). The cost of migration: spoonbills suffer higher mortality during trans-Saharan spring migrations only. Biol. Lett. 11: 20140944
Lok T, Overdijk O, Piersma T. (2013). Migration Tendency Delays Distributional Response to Differential Survival Prospects along a Flyway. The american Naturalist 181(4): 520-531
Sanz-Aguilar A, Béchet A, Germain C, Johnson AR, Pradel R (2012) To leave or not to leave: survival tradeoffs between different migratory strategies in the Greater Flamingo. Journal of Animal Ecology. 10.1111/j.1365-2656.2012.01997.x
Robust design:
Kendall WL, White GC, Hines JE, Langtimm CA, Yoshizaki J (2012). Estimating parameters of hidden Markov models based on marked individuals: use of robust design data. Ecology 93:913-920.
Senescence:
Choquet R, Viallefont A, Rouan L, Gaanoun K, Gaillard JM (2011). A semi-Markov model to assess reliably survival patterns from birth to death in free-ranging populations. Methods in Ecology and Evolution 2:383-389. 10.1111/j.2041-210X.2011.00088.x
Marzolin G, Charmantier A, Gimenez O (2011). Frailty in state-space models: application to actuarial senescence in the Dipper. Ecology 92:562-567. 10.1890/10-0306.1
Peron G, Crochet PA, Choquet R, Pradel R, Lebreton JD, Gimenez O (2010). Capture-recapture models with heterogeneity to study survival senescence in the wild. Oikos 119:524-532. 10.1111/j.1600-1706.2009.17882.x
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