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…

Conference Presentations

I recently gave a talk at the Ecological Society of America (ESA) annual meeting in Portland, OR and a poster presentation at the World Congress of Herpetology meeting in Vancouver, BC, Canada. Both presentations were comparing generalized linear mixed models (GLMM) and generalized estimating equations (GEE) for analyzing repeated count data. I advocate for using…

GLMM vs GEE plot with 95% confidence intervals

Plotting 95% Confidence Bands in R

I am comparing estimates from subject-specific GLMMs and population-average GEE models as part of a publication I am working on. As part of this, I want to visualize predictions of each type of model including 95% confidence bands. First I had to make a new data set for prediction. I could have compared fitted values…

Model Validation: Interpreting Residual Plots

When conducting any statistical analysis it is important to evaluate how well the model fits the data and that the data meet the assumptions of the model. There are numerous ways to do this and a variety of statistical tests to evaluate deviations from model assumptions. However, there is little general acceptance of any of…

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…