Paper Summary: Natural Disturbance and Logging Effects on Salamanders

Paper Summary: Hocking, D.J., K.J. Babbitt, and M. Yamasaki. 2013. Comparison of Silvicultural and Natural Disturbance Effects on Terrestrial Salamanders in Northern Hardwood Forests. Biological Conservation 167:194-202. doi: http://dx.doi.org/10.1016/j.biocon.2013.08.006 Unfortunately, this paper is behind a paywall. Please email me if you would like a copy for educational purposes. We were interested in how red-backed salamanders…

Installing and Running JAGS on Mac OS 10.5.8

JAGS is an alternative to BUGS (WinBUGS or OpenBUGS) for conducting a Bayesian Analysis. It stands for Just Another Gibbs Sampler, and like WinBUGS, it is essentially an MCMC machine that employs a Gibbs sampler so you don’t have to write your own for every analysis. JAGS code is very similar to the more popular…

GLMM Hell

I have been starting to analyze some data I have of repeated counts of salamanders from 5 plots over 4 years. I am trying to develop a predictive model of salamander nighttime surface activity as a function of weather variables. The repeated counting leads to the need for Generalized Linear Mixed Models (GLMM). Count data…

JAGS – Bayesian Analysis

JAGS is used for Bayesian analysis using MCMC and stands for Just Another Gibbs Sampler.  It is an alternative to WinBUGS and can be accessed through R just like WinBUGS (via R2jags or RJags).  It will work on a Mac unlike WinBUGS.  The only problem is that most books include WinBUGS examples and not JAGS…

Another boring blog

I recently decided to create two blogs as outlets for my research.  The first (The Richness of Life) focuses more on the organisms I work with as an ecologist and my general interest as a student of natural history.  This blog on Quantitative Ecology stems from my recent obsessive frustration with analyzing various data sets. …