889 research outputs found
Why do birds sing in such complex ways? – Bird Song: Biological Themes and Variations by Catchpole & Slater (2008)
No full textC. K. Catchpole & P. J. B. Slater 2008: Bird Song. Biological Themes and Variations. Second Edition. — Cambridge University Press
Modelling banding effect and tag loss for Little Penguins, Eudyptula minor, using Matlab
No full textWe present a framework for using Matlab to analyse mark-recapture data arising from studies that use more than one type of tag to mark animals for later identification. We consider life history data collected for groups of single and double tagged animals. We include tag loss probabilities in the likelihood function, which removes a common source of bias in the estimation of survival rates. We show how the formation of appropriate summary statistics, and use of vectorisation, vastly improves speed in computing the likelihood function. We illustrate our methods by analysing seven years of mark-recapture data for 2483 Little Penguins Eudyptula minor on Phillip Island in south-eastern Australia.
References D. G. Ainley, R. E. LeResche, and W. J. L. Sladen. Breeding Biology of the Adelie Penguin. University of California Press, Berkeley, 1983. A. N. Arnason and K. H. Mills. Bias and loss of precision due to tag loss in Jolly--Seber estimates for mark-recapture experiments. Canadian Journal of Fisheries and Aquatic Sciences, 38:1077--1095, 1981. doi:10.1139/f81-148 R. J. H. Beverton and S. J. Holt. On the dynamics of exploited fish populations. Fishery Investigations Series II, 19:1--533, 1957. doi:10.2307/1440619 C. J. A. Bradshaw, R. J. Barker, and L. S. Davis. Modeling tag loss in New Zealand fur seal pups. Journal of Agricultural, Biological and Environmental Statistics, 5(4):475--485, 2000. doi:10.2307/1400661 E. A. Catchpole. Ted Catchpole's Personal Home Page. http://pems.unsw.adfa.edu.au//staff/profiles/catchpole_t. E. A. Catchpole, S. N. Freeman, B. J. T. Morgan, and M. P. Harris. Integrated recovery/recapture data analysis. Biometrics, 54:33--46, 1998. doi:10.2307/2533993 E. A. Catchpole, B. J. T. Morgan, and G. Tavecchia. A new method for analysing discrete life-history data with missing covariate values. Journal of Royal Statistical Society, B, 70(2):445--460, 2008. doi:10.1111/j.1467-9868.2007.00644.x P. B. Conn, W. L. Kendall, and M. D. Samuel. A general model for the analysis of mark-resight, mark-recapture, and band-recovery data under tag loss. Biometrics, 60:900--909, 2004. doi:10.1111/j.0006-341X.2004.00245.x B. M. Culik, R. P. Wilson, and R. Bannasch. Flipper-bands on penguins: what is the cost of a life-long commitment? Marine Ecology Progress Series, 98:209--214, 1993. doi:10.3354/meps098209 P. Dann and J. M. Cullen. Survival, patterns of reproduction and lifetime reproductive output in the Little Blue Penguins (Eudyptula minor) on Phillip Island, Victoria, Australia. In L. S. Davis and J. T. Darby, editors, Penguin Biology, pages 63--84. Academic Press, San Diego, 1990. P. Dann, J. M. Cullen, and R. Jessop. Cost of reproduction in Little Penguins. In P. Dann, F. I. Norman, and P. N. Reilly, editors, The Penguins: Ecology and Management, pages 39--55. Surrey Beatty, Sydney, 1995. P. Dann, L. A. Sidhu, R. Jessop, L. Renwick, M. Healy, P. Collins, B. Baker, and E. A. Catchpole. The effects of flipper bands on the survival of adult Little Penguins Eudyptula minor. The Auk. In review. G. Froget, M. Gauthier-Clerc, Y. Le Maho, and Y. Handrich. Is penguin banding harmless? Polar Biology, 20:409--413, 1998. doi:10.1007/s003000050322 M. Gauthier-Clerc, J.-P. Gendner, C. A. Ribic, W. R. Fraser, E. J. Woehler, S. Descamps, C. Gilly, C. Le Bohec, and Y. Le Maho. Long-term effects of flipper bands on penguins. Proceedings of the Royal Society of London B (Supplement), Biology Letters, 271:423--426, 2004. doi:10.1098/rsbl.2004.0201 S. R. Johnson, J. O. Schiek, and G. F. Searing. Neck band loss rates for lesser snow geese. Journal of Wildlife Management, 59:747--752, 1995. doi:10.2307/3801951 R. King, S. P. Brooks, and T. Coulson. Analyzing complex capture-recapture data in the presence of individual and temporal covariates and model uncertainty. Biometrics, 64:1187--1195, 2008. doi:10.1111/j.1541-0420.2008.00991.x J.-D. Lebreton, K. P. Burnham, J. Clobert, and D. R. Anderson. Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological Monographs, 62:67--118, 1992. doi:10.2307/2937171 S. L. Petersen, G. M. Branch, D. G. Ainley, P. D. Boersma, J. Cooper, and E. J. Woehler. Is flipper banding of penguins a problem? Marine Ornithology, 33:75--79, 2005. http://marineornithology.org/PDF/33_2/33_2_75-79.pdf P. N. Reilly and J. M. Cullen. The Little Penguin Eudyptula minor in Victoria. I: Mortality of adults. Emu, 79:97--102, 1979. doi:10.1071/MU9790097 P. N. Reilly and J. M. Cullen. The Little Penguin Eudyptula minor in Victoria. II: Breeding. Emu, 81:1--19, 1981. doi:10.1071/MU9810001 P. N. Reilly and J. M. Cullen. The Little Penguin Eudyptula minor in Victoria. IV: Moult. Emu, 83:94--98, 1983. doi:10.1071/MU9830094 C. Saraux, C. Le Bohec, J. M. Durant, V. A. Viblanc, M. Gauthier-Clerc, D. Beaune, Y.-H. Park, N. G. Yoccoz, N. C. Stenseth, and Y. Le Maho. Reliability of flipper-banded penguins as indicators of climate change. Nature, 469:203--206, 13 January 2011. doi:10.1038/nature09630 G. A. F. Seber. The Estimation of Animal Abundance and Related Parameters. Griffin, London, 2nd edition, 1982. L. A. Sidhu, E. A. Catchpole, and P. Dann. Mark-recapture-recovery modeling and age-related survival in Little Penguins Eudyptula minor. The Auk, 124:815--827, 2007. doi:10.1642/0004-8038(2007)124[815:MMAASI]2.0.CO;2 W. T. Stobo and J. K. Horne. Tag loss in grey seals (Halichoerus grypus) and potential effects on population estimates. Canadian Journal of Zoology, 72:555--561, 1994. doi:10.1139/z94-075 R. J. Treble, R. W. Day, and T. J. Quinn II. Detection and effects on mortality estimates of changes in tag loss. Canadian Journal of Fisheries and Aquatic Sciences, 50:1435--1441, 1993. doi:10.1139/f93-164 J. A. Wetherall. Analysis of double-tagging experiments. Fishery Bulletin, 80:687--701, 1982. http://swfsc.noaa.gov/publications/CR/1982/8247.PDF Y. Xiao. A general model for estimating tag-specific shedding rates and tag interactions from exact or pooled times at liberty for a double tagging experiment. Canadian Journal of Fisheries and Aquatic Sciences, 53:1852--1861, 1996. doi:10.1139/cjfas-53-8-185
sj-pdf-1-jhi-10.1177_14604582211073075 – Supplemental Material for Display and perception of risk: Analysis of decision support system display and its impact on perceived clinical risk of sepsis-induced health deterioration
No full textSupplemental Material, sj-pdf-1-jhi-10.1177_14604582211073075 for Display and perception of risk: Analysis of decision support system display and its impact on perceived clinical risk of sepsis-induced health deterioration by Muge Capan, Laura C Schubel, Ishika Pradhan, Ken Catchpole, Nawar Shara, Ryan Arnold, J Sanford Schwartz¸Jake Seagull, Kristen Miller in Health Informatics Journal</p
sj-pdf-2-jhi-10.1177_14604582211073075 – Supplemental Material for Display and perception of risk: Analysis of decision support system display and its impact on perceived clinical risk of sepsis-induced health deterioration
No full textSupplemental Material, sj-pdf-2-jhi-10.1177_14604582211073075 for Display and perception of risk: Analysis of decision support system display and its impact on perceived clinical risk of sepsis-induced health deterioration by Muge Capan, Laura C Schubel, Ishika Pradhan, Ken Catchpole, Nawar Shara, Ryan Arnold, J Sanford Schwartz¸Jake Seagull, Kristen Miller in Health Informatics Journal</p
Group of women after baseball game
No full textLeft to right: Mrs. J. Purser, E. De Wolf, E. Catchpole, G. Collett, G. Belshaw, Mrs. Dobson, Mrs. Wallace
Abalone I: Analyzing Mark-Recapture-Recovery Data Incorporating Growth and Delayed Recovery
No full textAbalone are semimobile marine gastropods that form the basis of Australia's second most valuable fishery. A site off the coast of Port Arthur. Tasmania, was visited on six occasions. On each occasion, any unmarked live abalone found were marked with a unique identification number and were recorded. Any previously marked abalone found had its identification number and whether or not it was still alive recorded. This results in integrated mark-recapture-recovery data, as in Catchpole et al. (1998, Biometrics 54, 33-46). During the study period, abalone grew in size, and we model the survival of individuals as a function of their size? estimated from a fitted growth curve. The shells of dead animals are long lasting, and we extend existing methodology to allow for the possibility that an animal found dead may have been dead but overlooked for several visits
Parameter Identifiability and Redundancy: Theoretical Considerations
No full textBackground - Models for complex biological systems may involve a large number of parameters. It may well be that some of these parameters cannot be derived from observed data via regression techniques. Such parameters are said to be unidentifiable, the remaining parameters being identifiable. Closely related to this idea is that of redundancy, that a set of parameters can be expressed in terms of some smaller set. Before data is analysed it is critical to determine which model parameters are identifiable or redundant to avoid ill-defined and poorly convergent regression.
Methodology/Principal Findings - In this paper we outline general considerations on parameter identifiability, and introduce the notion of weak local identifiability and gradient weak local identifiability. These are based on local properties of the likelihood, in particular the rank of the Hessian matrix. We relate these to the notions of parameter identifiability and redundancy previously introduced by Rothenberg (Econometrica 39 (1971) 577–591) and Catchpole and Morgan (Biometrika 84 (1997) 187–196). Within the widely used exponential family, parameter irredundancy, local identifiability, gradient weak local identifiability and weak local identifiability are shown to be largely equivalent. We consider applications to a recently developed class of cancer models of Little and Wright (Math Biosciences 183 (2003) 111–134) and Little et al. (J Theoret Biol 254 (2008) 229–238) that generalize a large number of other recently used quasi-biological cancer models.
Conclusions/Significance - We have shown that the previously developed concepts of parameter local identifiability and redundancy are closely related to the apparently weaker properties of weak local identifiability and gradient weak local identifiability—within the widely used exponential family these concepts largely coincide
The effect of directional wind components on survival of Little Penguins Eudyptula minor
No full textWe live in an age of increased awareness of climate change and its potential effects on our ecosystems. Here we look at the effect of one aspect of climate, directional wind components, on the survival of Little Penguins Eudyptula minor on Phillip Island in south-eastern Australia, using mark-recapture data gathered over a 42 year period since 1968. We apply biologically realistic age structures for the survival and recapture probabilities, and use mean seasonal wind magnitudes from the four cardinal compass directions as covariates in our modelling of the survival probability. Results indicate that first year survival is most affected by southerly winds in the winter prior to the chick's birth, which increase survival, and by easterly winds in the summer of hatching/fledging, which decrease survival. Adult survival is most affected by increasing northerly winds in the autumn following moult (positively) and by easterly winds in the preceding summer (negatively). For both first-year and adult birds, increasing easterly summer wind is associated with decreased survival, possibly due to reduced flows of nutrient rich waters from western Bass Strait.
References D. G. Ainley, J. Russell, S. Jenouvrier, E. Woehler, P. O. Lyver, W. R. Fraser, and G. L. Kooyman. Antarctic penguin response to habitat change as earth's troposphere reaches C above preindustrial levels. Ecological Monographs, 80:49--66, 2010. http://www.esajournals.org/doi/pdf/10.1890/08-2289.1 C. J. Brown, E. A. Fulton, A. J. Hobday, R. J. Matear, H. P. Possingham, C. Bulman, V. Christensen, R. E. Forrest, P. C. Gehrke, N. A. Gribble, S. P. Griffiths, H. Lozano-Montes, J. M. Martin, S. Metcalf, T. A. Okey, R. Watson, and A. J. Richardson. Effects of climate--driven primary production changes on marine food webs: implications for fisheries and conservation. Global Change Biology, 16:1194--1212, 2010. doi:10.1111/j.1365-2486.2009.02046.x K. Burnham and D. Anderson. Model selection and multimodel inference: a practical information-theoretic approach. Springer Verlag, 2002. E. A. Catchpole, S. N. Freeman, B. J. T. Morgan, and M. P. Harris. Integrated recovery/recapture data analysis. Biometrics, 54:33--46, 1998. doi:10.2307/2533993 L. E. Chambers, C. A. Devney, B. C. Congdon, N. Dunlop, E. J. Woehler, and P. Dann. Observed and predicted effects of climate on Australian seabirds. Emu, 111:235--251, 2011. doi:10.1071/MU10033 M. Collins, J. M. Cullen, and P. Dann. Seasonal and annual foraging movements of Little Penguins from Phillip Island, Victoria. Wildlife Research, 26:705--721, 1999. doi:10.1071/WR98003 R. M. Cormack. Estimates of survival from the sighting of marked animals. Biometrika, 51:429--438, 1964. doi:10.1093/biomet/51.3-4.429 J. M. Cullen, L. E. Chambers, P. C. Coutin, and P. Dann. Predicting onset and success of breeding in little penguins Eudyptula minor from ocean temperatures. Marine Ecology Progress Series, 378:269--278, 2009. doi:10.3354/meps07881 P. Dann. An experimental manipulation of clutch size in the Little Penguin Eudyptula minor. Emu, 88:101--103, 1988. doi:10.1071/MU9880101 P. Dann. Distribution, population trends and factors influencing the population size of Little Penguins Eudyptula minor on Phillip Island, Victoria. Emu, 91(5):263--272, 1992. doi:10.1071/MU9910263 P. Dann and J. M. Cullen. Survival, patterns of reproduction and lifetime reproductive output in the Little Blue Penguins (Eudyptula minor) on Phillip Island, Victoria, Australia. In L. S. Davis and J. T. Darby, editors, Penguin Biology, pages 63--84. Academic Press, San Diego, 1990. P. Dann, J. M. Cullen, R. Thoday, and R. Jessop. Movements and patterns of mortality at sea of Little Penguins Eudyptula minor from Phillip Island, Victoria. Emu, 91(5):278--286, 1992. doi:10.1071/MU9910278 S. T. Garnett and G. M. Crowley. The Action Plan for Australian Birds 2000. Environment Australia, Canberra, 2000. http://www.environment.gov.au/biodiversity/threatened/publications/action/birds2000/index.html K. E. Harrigan. Causes of mortality of Little Penguins Eudyptula minor in Victoria. Emu, 91:273--277, 1992. A. J. Hoskins, P. Dann, Y. Ropert-Coudert, A. Kato, A. Chiaradia, D. P. Costa, and J. P. Y. Arnould. Foraging behaviour and habitat selection at sea in Little Penguins Eudyptula minor during the chick-guard stage of breeding. Marine Ecology Progress Series, 366:293--303, 2008. G. M. Jolly. Explicit estimates from capture-recapture data with both death and immigration-stochastic models. Biometrika, 52:225--247, 1965. doi:10.2307/2333826 B. R. King, J. T. Hicks, and J. Cornelius. Population changes, breeding cycles and breeding success over six years in a seabird colony at Michaelmas Cay, Queensland. Emu, 92:1--10, 1992. doi:10.1071/MU9920001 P. McCullagh and J. A. Nelder. Generalized Linear Models. Chapman and Hall, London, 2nd edition, 1989. C. McCutcheon, P. Dann, M. Salton, L. Renwick, A. J. Hoskins, A. M. Gormley, and J. P. Y. Arnould. The foraging range of Little Penguins (Eudyptula minor) during winter. Emu (online first), 2011. doi:10.1071/MU10078 M. J. Mickelson, P. Dann, and J. M. Cullen. Sea temperature in Bass Strait and breeding success of the Little Penguins Eudyptula minor at Phillip Island, South-eastern Australia. Emu, 91(5):355--368, 1992. doi:10.1071/MU9910355 I. C. T. Nisbet and P. Dann. Reproductive performance of little penguins in relation to year, age, pair-bond duration, breeding date and individual quality. Journal of Avian Biology, 40:296--308, 2009. doi:10.1111/j.1600-048X.2008.04563.x P. N. Reilly and J. M. Cullen. The Little Penguin Eudyptula minor in Victoria. {II}: Breeding. Emu, 81:1--19, 1981. doi:10.1071/MU9810001 Y. Ropert-Coudert, A. Kato, and A. Chiaradia. Impact of small-scale environmental perturbations on local marine food resources: a case study of a predator, the little penguin. In Proceedings of the Royal Society B, volume 276, pages 4105--4109, 2009. doi:10.1098/rspb.2009.1399 P. A. Sandery. Seasonal variability of water mass properties in Bass Strait: three-dimensional oceanographic modelling studies. PhD thesis, Flinders University, Adelaide, 2007. http://catalogue.flinders.edu.au/local/adt/public/adt-SFU20070831.093503 G. A. F. Seber. A note on the multiple recapture census. Biometrika, 52:249--259, 1965. doi:10.1093/biomet/52.1-2.249 L. A. Sidhu. Analysis of recovery-recapture data for Little Penguins. PhD thesis, School of Physical, Environmental and Mathematical Sciences, The University of New South Wales at the Australian Defence Force Academy, 2007. L. A. Sidhu, E. A. Catchpole, and P. Dann. Mark-recapture-recovery modeling and age-related survival in Little Penguins Eudyptula minor. The Auk, 124:815--827, 2007. doi:10.1642/0004-8038(2007)124[815:MMAASI]2.0.CO;2 L. A. Sidhu, E. A. Catchpole, and P. Dann. Modelling banding effect and tag loss for Little Penguins Eudyptula minor. In W. McLean and A. J. Roberts, editors, Proceedings of the 15th Biennial Computational Techniques and Applications Conference, CTAC-2010, volume 52 of ANZIAM Journal, pages C206--C221, 2011. http://journal.austms.org.au/ojs/index.php/ANZIAMJ/article/view/3941 [June 6, 2011]
Modelling age variation in survival and reporting rates for recovery models
No full textIn this paper, we focus on models for recovery data from birds ringed as young. In some cases, it is important to be able to include in these models a degree of age variation in the reporting probability. For certain models this has been found, empirically, to result in completely flat likelihood surfaces, due to parameter redundancy. These models cannot then be fitted to the data, to produce unique parameter estimates. However, empirical evidence also exists that other models with such age variation can be fitted to data by maximum likelihood. Using the approach of Catchpole and Morgan (1996b), we can now identify which models in this area are parameter-redundant, and which are not. Models which are not parameter-redundant may still perform poorly in practice, and this is investigated through examples, involving both veal and simulated data. The Akaike Information Criterion is found to select inappropriate models in a number of instances. The paper ends with guidelines for fitting models to data from birds ringed as young, when age dependence is expected in the reporting probability
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