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Markov Chain Nest Productivity Model (MCestimate)

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MCestimate is a tool for estimating probabilities of failure in the presence of competing risks. It was originally developed to facilitate the study of causes of avian nest-failure. However, competing risks arise in virtually all stochastic processes and MCestimate can be applied in many contexts outside of avian nest failure, including carcass-searches at anthropogenic hazards and correcting mortality estimates in laboratory toxicity tests.

The User’s Guide (PDF) (41 pp, 2.4 MB) introduces the model and provides step-by-step instructions on how to use it. The Technical Manual (PDF) (22 pp, 825 KB) provides most of the equations underlying the model.

MCestimate consists of a zip file and the Matlab Compiler Runtime (see instructions below for how to download this file from the Mathworks website). The MCestimate.zip file contains three files, MCestimate.exe, SimData.xls, and SimDataBad.xlsx.

MCestimate.zip (3 September 2013; 738 KB)

MCestimate was designed in Matlab R2012a and requires the Matlab Compiler Runtime (MCR) to be installed on your computer. MCestimate will not run without the MCR. Due to its size, we are not hosting the MCR on our website. It can be downloaded free of charge from the Mathworks website. The required version is the Windows 32-bit MCR for Matlab release 2012a.

MCestimate is a working model designed for research purposes. As such it changes constantly, and is updated whenever bugs are discovered.

Background references:

Custer, C., Custer, T.W., Dummer, P.W., Etterson, M.A., Thogmartin, W.E., Wu, Q. Kannan, K. Trowbridge, A. and McKann,P.A. In Press. Exposure and effects of perfluorinated compounds in tree swallows nesting in Minnesota and Wisconsin, USA. Archives of Environmental Contamination and Toxicology.

Etterson, M., L. Nagy, and T. Robinson. 2007. Partitioning risk among different sources of nest-failure. The Auk 124:432-443.

Etterson, M., B. Olsen, and R. Greenberg. 2007. The analysis of covariates in multi-fate Markov chain nest failure models. Studies in Avian Biology 34:55-64.

Jackson, A.K., D.C. Evers, M.A. Etterson, A.M. Condon, S.B. Folsom, J.Detweiler, J. Schmerfeld, and D.A. Cristol. 2011. Mercury exposure affects the reproductive success of a free-living terrestrial songbird, the Carolina Wren (Thryothorus ludovicianus). Auk 128:759-769.

Johnson, T.N, P.L. Kennedy, and M.A. Etterson. 2012 Factors influencing cause-specific nest-failure of grassland passerines in grazed prairie. Journal of Wildlife Management 76:1607-1616.

For further information, please contact Matt Etterson etterson.matthew@epa.gov, (218) 529-5158.

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