Author Archives: Simon Bonner
Having started and stopped many times I’ve decided that I am finally going learn to use python. I’m a devoted emacs user and I love my Surface Pro 4, but I also prefer Linux to Windows, so my setup is … Continue reading
Congratulations to Alex Draghici who also passed his PhD proposal defense today. Two in 24 hours. It’s a privilege to work with such excellent students!
Adding patchwork to the list of my favourite R packages. Don’t let the syntax fool you. This is an incredibly powerful package for arranging plots created with ggplot2. Check out the example here.
Congratulations to Hanna Kim who just passed her PhD proposal defence. Great job all around. I’m looking forward to seeing the work progress over the rest of your degree!
In the past I have always used is.null() in R to test whether a list contains a specified element. E.g., if I wanted to know whether a list, mylist contained the element x I would have used This failed me … Continue reading
Just stumbled across this article about former student Gabrielle Miles on the University of Kentucky’s website. Gabby is now a Senior Biostatistician with Roche Professional Diagnostics in Indianapolis.
Congratulations to Woody for successfully defending his PhD titled “Improving the Computational Efficiency in Bayesian Fitting of Cormack-Jolly-Seber Models with Individual, Continuous, Time-Varying Covariates” on May 26. His thesis is now available online through the University of Kentucky archives. Woody is … Continue reading
I wrote my first vignette for an R package the other day and was amazed at the ease of writing Rmarkdown. Of course, I am using emacs and was looking for a mode that would allow me to edit these … Continue reading
I have been working on simulating data from Bob Dorazio’s version of the Royle N-mixture model for repeated count data. This version of the model assumes that the abundance at site is generated from a Hurdle model such that and … Continue reading
The last time I worked with parallel processing in R I used the package Rmpi. This ws very flexible, but took a lot of setup to handle passing jobs, code, and data between the master and the slave. I have … Continue reading
The Charleston Gazette: Mountaintop removal: The scientific evidence of environmental and health damage continues
Brenee Muncy’s work also got mention in an article by Keith Ward Jr. published on the Charleston Gazette’s blog on October 23.
On October 31 Richard Conniff covered Brenee Muncy’s salamander work in an article published on Takepart — “a digital news & lifestyle magazine and social action platform for the conscious consumer”.
Mountaintop Removal Mining Reduces Stream Salamander Occupancy and Richness in Southeastern Kentucky (USA) Biological Conservation
Back at the end of September Brenee Muncy’s paper on the effects of mountain top mining on salamander occupancy was accepted for publication in Biological Conservation. The full text is now available online. This paper uses Bayesian occupancy models to … Continue reading
On October 27, Ben Augustine presented his work on mark-recapture models with behavioral effects and subsampling at the 2014 Annual Conference of The Wildlife Society in Pittsburgh, PA. This work has also been accepted for publication in Methods in Ecology … Continue reading
Accounting for Behavioral Response to Capture when Estimating Population Size from Hair Snare Studies with Missing Data
Ben Augustine’s paper on behavioral effects and subsampling has been accepted for publication in Methods in Ecology and Evolution and is now available online. The work is particularly applicable to studies which use hair snares to capture animals. Snares are … Continue reading
We continued our discussion of prior distributions for mark-recapture models including covariates in lab today by looking at the paper A Weakly Informative Default Prior Distribution for Logistic and Other Regression Models published by Andrew Gelman et al in the … Continue reading