Readings on Statistics and Biology

Frequentist approaches, likelihood methods, information theory, and Bayesian statistics

Short courses:
Likelihood methods in ecology at Cary Institute of Ecosystem Studies (link)

Newer references: books
Anderson, D.R. 2008. Model Based Inference in the Life Sciences: A Primer on Evidence. Springer. 184 pp.
Clark, J.S.  2007.  Models for ecological data: an introduction.  Princeton University Press. 632 pp.
Congdon, P. 2006. Bayesian Statistical Modeling. Second Edition. John Wiley& Sons, Sussex, England.  573 pp.

Newer references: papers
Elliott, L. P. and Brook, B. W. 2007. Revisiting Chamberlin: multiple working hypotheses for the 21st centuryBioscience 57: 608-614.
Martınez-Abraın, A. 2007. Are there any differences? A non-sensical question in ecology. Acta Oecologica 32: 203–206.
Stephens, P. A., Buskirk, S. W. and Del Rio, C. M. 2007. Inference in ecology and evolution. Trends in Ecology & Evolution 22: 192-197.
Stephens, P. A., Buskirk, S. W., Hayward, G. D. and Del Rio, C. M. 2007. A call for statistical pluralism answered. Journal of Applied Ecology 44: 461-463.
Stephens, P. A., Buskirk, S. W., Hayward, G. D. and Del Rio, C. M. 2005. Information theory and hypothesis testing: a call for pluralism. Journal of Applied Ecology 42: 4-12.
Richards, S. A. 2005. Testing ecological theory using the information-theoretic approach: examples and cautionary resultsEcology 86: 2805-2814.
Berger, James O.  2002.  Could Fisher, Jeffreys, and Neyman have agreed on testing?.  Statistical Science 18: 1-12.  Link to alternative pdf.  See comments by 8 other authors and rejoinder by Berger (link via jstor).

Journal club readings for discussion of 1 October 2004
Anderson, D.R., K.P. Burnham, and W. L. Thompson. 2000. Null hypothesis testing: problems, prevalence, and an alternative. Journal of Wildlife Management 64:912-923. Read abstract only.
Ellison, A. M. 2004. Bayesian inference in ecology. Ecology Letters 7:509-520.
Johnson, J. B. and K. S. Omland. 2004. Model selection in ecology and evolution. Trends in Ecology & Evolution 19:101-108.

Some related references for zealots, in reverse chronology
Gotelli, N.J., and A. M. Ellison. 2004. A primer of ecological statistics. Sinauer Associates. Sunderland MA.
Hubbard, R. 2004. Blurring the distinctions between p's and alpha's in psychological research. Theory & Psychology 14:295-327.
Mogie, M. 2004. In support of null hypothesis significance testing. Proceedings of the Royal Society of London Series B-Biological Sciences 271:S82-S84.
Fidler, F., N. Thomason, G. Cumming, S. Finch, and J. Leeman. 2004. Editors can lead researchers to confidence intervals, but can't make them think - statistical reform lessons from medicine. Psychological Science 15:119-126.
Di Stefano, J. 2004. A confidence interval approach to data analysis. Forest Ecology and Management 187:173-183.
Brooks, S. P. 2003. Bayesian computation: a statistical revolution. Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences 361:2681-2697.
Godinez-Dominguez, E. and J. Freire. 2003. Information-theoretic approach for selection of spatial and temporal models of community organization. Marine Ecology-Progress Series 253:17-24.
Eberhardt, L. L. 2003. What should we do about hypothesis testing? Journal of Wildlife Management 67:241-247.
Dorazio, R. M. and F. A. Johnson. 2003. Bayesian inference and decision theory - a framework for decision making in natural resource management. Ecological Applications 13:556-563.
Gould, W. R. and R. L. Steiner. 2002. Viewpoint: improving range science through the appropriate use of statistics. Journal of Range Management 55:526-529.
Boyce, M. S. 2002. Statistics as viewed by biologists. Journal of Agricultural Biological and Environmental Statistics 7:306-312.
Anderson, D. R. and K. R. Burnham. 2002. Avoiding pitfalls when using information-theoretic methods. Journal of Wildlife Management 66:912-918.
Pigliucci, M. 2002. Are ecology and evolutionary biology "soft" sciences? Annales Zoologici Fennici 39:87-98.
Robinson, D. H. and H. Wainer. 2002. On the past and future of null hypothesis significance testing. Journal of Wildlife Management 66:263-271.
Johnson, D. H. 2002. The role of hypothesis testing in wildlife science. Journal of Wildlife Management 66:272-276.
Steury, T. D., A. J. Wirsing, and D. L. Murray. 2002. Using multiple treatment levels as a means of improving inference in wildlife research. Journal of Wildlife Man

Link to this topic in Bio 125: The Nature and Practice of Science
Meeting 4;   Meetings 5-6