Jingwa A, Brian (2011): Improving biodiversity monitoring by modeling relative abundance from "presence only" data. Published in: tUL Diepenbeek No. 2011 (2011)
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One of the greatest concerns of this age is finding definitive ways to curb the loss of biodiversity. Although there have been growing calls on biodiversity protection and conservation by governments and institutions, the challenge lies on fitting models that best explain the trends of target species over space and time. The objective of this project was to determine the probability of detection of four species and how it changes with time during the season. Also, the occupancy of each species and its relationship with abundance was obtained. Siteoccupancy models were fitted to the data, with each model having four components; occupancy, colonization, extinction and detection probability. Model selection was done on the basis of the AIC criterion. The results show different trends for each species over time. The occupancies of each species do reflect the abundances in the various stages of their life cycles. The colonization, extinction and detection probability estimates were also obtained at each time point.
|Item Type:||MPRA Paper|
|Original Title:||Improving biodiversity monitoring by modeling relative abundance from "presence only" data|
|Keywords:||Presence-only data; data modelling; site occupancy; colonization; extinction; detection probability; species abundance|
|Subjects:||C - Mathematical and Quantitative Methods > C3 - Multiple or Simultaneous Equation Models ; Multiple Variables > C32 - Time-Series Models ; Dynamic Quantile Regressions ; Dynamic Treatment Effect Models ; Diffusion Processes ; State Space Models
Y - Miscellaneous Categories > Y4 - Dissertations (unclassified) > Y40 - Dissertations (unclassified)
C - Mathematical and Quantitative Methods > C5 - Econometric Modeling > C50 - General
C - Mathematical and Quantitative Methods > C5 - Econometric Modeling > C52 - Model Evaluation, Validation, and Selection
Q - Agricultural and Natural Resource Economics ; Environmental and Ecological Economics > Q5 - Environmental Economics
|Depositing User:||Brian A. Jingwa|
|Date Deposited:||06. Dec 2011 14:05|
|Last Modified:||03. May 2015 20:21|
Betts, M., Rodenhouse , N., Sillett, S., Doran, P. and Holmes, R. (2008) Dynamic occupancy models reveal within-breeding season movement up a habitat quality gradient by migratory songbird. Ecography 31, 592-600.
Chakraborty, A., Gelfand, A., Wilson, A., Latimer, A. and Silander J. (2011) Poing pattern modelling for degraded presence-only data over large regions to appear. Journal of Royal Society, Series C.
Elith, J., Graham, C., Anderson, R., Dudk, M., Ferrier, S., Guisan, A., Hijmans, R., Huettmann, F., Leathwick, J., Lehmann, A., Li, J., Lohmann, L., Loiselle, B., Manion, G., Moritz, C., Nakamura, M., Nakazawa, Y., Overton, J., Peterson, A., Phillips, S., Richardson, K., Scachetti-Pereira, R., Schapire, R., Sober´on, J., Williams, S., Wisz, M., and Zimmermann, N. (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography, 29, 129–151.
European Commission. (2011) communication from the commission to the European parliament, the council, the economic and social committee and the committee of the regions our life insurance, our natural capital: an EU biodiversity strategy to 2020. Com 244.
Gaston, K., Blackburn, T., Greenwood, J., Gregory, R., Quinn, R. and Lawton, J. (2000) Abundance-occupancy relationships. Journal of Applied Ecology, 37, 39-59.
Gelfand, A., Schmidt, A., Wu, S. and Rebelo, A. (2003) Modelling species diversity through level hierarchical modelling. Appl. Statist, 54, 1-20
Guisan, A. and Zimmermann, N. (2000) predictive habitat distribution models in ecology. Ecological Modelling, 135, 147-186.
Herremans, M. (2009) Monitoring using waarnemingen.be. Natuur.oriolus 76(3), 94-108.
Herremans, M. (2010) Is the Kestrel hovering on the brink ? Natuur.oriolus 77(2), 60-67.
Keating K., and Cherry S. (2004) Use and interpretation of logistic regression in habitat-selection studies. Journal of Wildlife Management, 68(4), 774-789.
Kéry, M., Royle, A. and Schmid, H. (2005) Modelling avian abundance from replicated counts using binomial mixture models. Ecological Applications, 15(4), 1450-1461.
Kéry, M., Royle, A. and Schmid, H. (2006) Estimating species richness: calibrating a large avian monitoring program. Journal of applied ecology, 43, 101-110.
Kéry, M., Royle, A., Schmid, H., Volet, B., Hafliger, G. and Zbinden N. (2009) Site-occupancy distribution to correct population-trend derived from opportunistic observations. Conservational Biology, 1388-1397.
MacKenzie, D and Bailey, L. (2004) Assessing the fit of site-occupancy models. Journal of Agricultural, biological and Environmental Statistics, 9(3), 300-318.
MacKenzie, D. (2005) Was it there? Dealing with imperfect detection for species presence/absence data. Aust. N.Z.J. Stat. 47(1), 65-74.
MacKenzie, D., Kendall, W. (2002) How should detection probability be incorporated into estimates of relative abundance. Ecology, 83(9), 2387-2393.
MacKenzie, D., Nicholas, J., Hines, J., Knutson, M., Franklin, A. (2003) Estimating site occupancy, colonization and local extinction when a species is detection imperfectly. Ecology, 84(8), 2200-2207.
MacKenzie, D., Nichols, J., Lachman, G., Droege, S., Royle, A. and Langtimm, C. (2002) Estimating site occupancy when detection probabilities are less than one. Ecology, 83, 2248-2255.
Nazeri, M., Jusoff, K., Bahaman, A. and Madani, N. (2010) Modelling the potential distribution of wildlife species in the tropics. World Journal of Zoology, 5(3), 225-231.
Niemela, J. (2000) Biodiversity monitoring for decision making. Ann. Zool. Fennici, 37, 307-317.
Ottaviani, D., Lasinio, G. and Boitani, L. (2004) Two statistical methods to validate habitat suitability models using presence-only data. Ecological Modelling, 179, 417-443.
Pearce, J. and Boyce M. (2003) Modelling distribution and abundance with presence-only data. Journal of Applied Ecology, 43, 405-412.
Royle, A. and Nichols, J. (2003) Estimating abundance from repeated presence-absence data or point counts. The Ecological Society of America, 84(3), 777-790.
Royle, A. and Kéry, M. (2007) A baysian state-space formulation of dynamic occupancy models. Ecology, 88(7), 1813-1823.
Royle, A., Nicholas, D. and Kéry, M. (2005) Modelling occurrence and abundance of species when detection is imperfect. Oikos, 110, 353-359.
Stork, N. and Samways, M. (1995) Inventory and monitoring. Global Biodiversity Assessment, 453-543.
Warton, D. and Shepherd, L. (2010) Poisson point process models solve the “pseudo-absence problem” for presence-only data in ecology. The Annals of Applied Statistics, 4(3), 1383-1402
Wintle, B., McCarthy, M., Parris, K. and Burgman, M. (2004) Precision and bias of methods for estimating point survey detection probabilities. Ecological Applications 14(3), 703-712.
Zaniewski, E., Lehmann, A., and Overton, J. (2002) Predicting species spatial distributions using presence-only data: a case study of native New Zealand ferns. Ecological Modelling, 157, 261-280.
Dorazio, R., Gotelli, N. and Ellison, A. (2011) Modern Methods of Estimating Biodiversity from Presence-Absence Surveys. Biodiversity / Book 4, O. Grillo (ed.)
MacKenzie, D., Nichols J., Royle A., Pollock, K., Bailey L., and Hines J. (2006) Occupancy Estimation and Modelling: Inferring Patterns and Dynamics of Species Occurrence. Elsevier Inc.
Donovan, T. and J. Hines. (2007) Exercises in occupancy modelling and estimation. http://www.uvm.edu/envnr/vtcfwru/spreadsheets/occupancy.htm (Accessed on 19/07/2011)
World Resource Institute http://archive.wri.org/page.cfm?id=535&page=pubs_content_text (Accessed on 19/08/2011)
World Resource Institute http://www.conservation.org/learn/biodiversity/Pages/overview.aspx (Accessed on 25/07/2011)
European Commission 2008: The Global Cost of Biodiversity Loss: 14 Trillion Euros? Science for Environmental Policy
World Wide Fund for Nature http://wwf.panda.org/about_our_earth/biodiversity/threatsto_biodiversity/ (Accessed on 20/08/2011)
Convention on Biological Diversity 2010 http://www.conservation.org/newsroom/pressreleases/Pages/World-Governments-Fail-Deliver-2010-Biodiversity-Target.aspx (Assessed on 25/07/2011)
Oiseau Rare. A French organisation for rare birds. http://www.ornitho.fr (Accessed on 10/07/2011)
Natuur Punt (Belgian nature point) www.natuurpunt.be (Assessed on 15/07/2011)
Perception website with records of species and perception times www.waarneming.be (Assessed on 05/07/2011)
US international bird tracking program EBIRD http://ebird.org (Assessed on 7/7/2011)
PRESENCE 2.0 http://www.mbr-pwrc.usgs.gov/software/presence.html
Words and Pictures http://www.wordsandpictures.me.uk/insects1a.html (Accessed on 13/07/2011)