15 April 2013


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Thinking about P-values

System administration

Set up accounts and begin installing software on antlab workstation. Had to install openssh-client to allow ssh access.


thinking about P-values and AIC

Shaw, R. G., & Geyer, C. J. (2010). Inferring fitness landscapes. Evolution, 64(9), 2510–2520. doi:10.1111/j.1558-5646.2010.01010.x

  • Limits to the number of preditors (traits) that can be practically analyzed by model comparison. Also a nice explanation of AIC and BIC.

Anderson, D. R., Burnham, K. P., & Thompson, W. L. (2000). Null hypothesis testing: problems, prevalence, and an alternative. Journal of Wildlife Management, 64(4), 912–923. Retrieved from http://www.jstor.org/stable/3803199

  • one of the early AIC papers by Anderson and Burnham

Johnson, J. B., & Omland, K. S. (2004). Model selection in ecology and evolution. Trends in Ecology and Evolution, 19(2), 101–8. doi:10.1016/j.tree.2003.10.013

  • overview of model selection methods

Gelman, A. (2013). P Values and Statistical Practice. Epidemiology, 24(1), 69–72. doi:10.1097/EDE.0b013e31827886f7

  • evaluation of what a P value is and isn’t

Stewart-Oaten, A. (1995). Rules and judgments in statistics: three examples. Ecology, 76(6), 2001–2009. Retrieved from http://www.jstor.org/stable/10.2307/1940736

  • Ecology classic. definitely cite to show how field has and has not changed in 13 years

Zuur, A., Ieno, E., & Elphick, C. (2010). A protocol for data exploration to avoid common statistical problems. Methods in Ecology and Evolution, 1(1), 3–14. doi:10.1111/j.2041-210X.2009.00001.x

  • title says it all


Cagliani, R., Pozzoli, U., Forni, D., Cassinotti, A., Fumagalli, M., Giani, M., Fichera, M., Lombardini, M., Ardizzone, S., Asselta, R., Franchis, R. de, Riva, S., Biasin, M., Comi, G.P., Bresolin, N., Clerici, M. & Sironi, M. (2013). Crohn’s Disease Loci Are Common Targets of Protozoa-Driven Selection. Molecular Biology and Evolution, 30, 1077–1087.

  • Yet more evidence linking common-disease to (interactions) with pathogens a la Paul Ewald

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