glmmADMB - WGSA Workshop Series

UPDATE: presentation from workshop

This week, for the WGSA Workshop Series, Cassie Jansch will be discussing the R package glmmADMB. This workshop will be Wednesday March 25th at 4:00pm in the Dean's Conference Room.

The R software package {glmmADMB} allows for fitting generalized linear mixed models (GLMMs) within the R interface with the power of AD Model Builder (a program that I will freely admit I don't understand) to a further extent than other packages such as {lme4} allow. For example, you can fit models with responses described by a negative binomial distribution that include multiple random effects with incorporated zero inflation. There are also a variety of response distributions (including Beta, truncated Poisson, Gamma,...) and link functions (log, logit, probit,...) at your beck and call. Familiarity with GLMs and GLMMs is helpful in learning how this package can work for you. To properly run {glmmADMB}, R package {R2admb} is required, and installing these two in advance will allow us to dive into the fun a little quicker!

install.packages("glmmADMB", repos="http://r-forge.r-project.org", type="source")​

install.packages("R2admb", repos="http://R-Forge.R-project.org")

Data files to download for the workshop:
intro_glmmadmb.R
countdata.csv

Please come by and check it out!

2015 Warnell Graduate Symposium

The Symposium starts tomorrow! This is one of the big academic events at Warnell that provides an opportunity to present the diverse research we are all working on with our peers. Often we find ourselves traveling to specific conferences to present to broader audiences engaged in our respective fields, which is wonderful but often creates a gap in the communication of research ideas within our own community. For those reasons, this even is such a great opportunity, not to mention a lot of fun! We will kick off the events tomorrow with the Colloquium speaker, Dr. William Uihlein, at 3:30 in room 1-304. Posters will be up in the lobby of building 4 from 1:00pm Wednesday through Friday, so please head over and take a look. Following the seminar tomorrow, we will meet for a poster session reception from 4:30-6:30. Please plan to attend the Colloquium address by Dr. Uihlein and then join us for a reception with your colleagues.

You can find a copy of the program here! There will be more than 50 students presenting on Tuesday, so please plan to attend to support the Warnell community to engage in the research happening right here at UGA!

Congrats to Derek Bahr

At the recent Southern Division AFS, our very own Derek Bahr was runner-up for the Best Student Presentation Award. Congrats Derek! The abstract of the talk he presented is below.

Atlantic Sturgeon recruitment in the Savannah River, Georgia

Derek L. Bahr

Warnell School of Forestry and Natural Resources–University of Georgia

180 E Green Street, Athens, GA 30602

Phone: (715) 869-0513

Email: dbahr286@uga.edu

Douglas L. Peterson

Warnell School of Forestry and Natural Resources–University of Georgia

180 E Green Street, Athens, GA 30602

Phone: (706) 542-2944

Email: dpeterson@warnell.uga.edu

Atlantic sturgeon were once abundant along the Atlantic Coast of North America from the Saint John River, Canada to the St. Johns River, Florida. Severe overfishing, coupled with habitat losses during the 1900s, resulted in major population declines that eventually led to the species’ listing under the US Endangered Species Act in 2012. Although Atlantic sturgeon are now considered endangered, quantified recruitment data are largely lacking for most systems, particularly among populations within the South Atlantic Distinct Population Segment (DPS). The objective of this study was to quantify annual recruitment of Atlantic sturgeon in the Savannah River, Georgia by estimating annual abundance of age-1 river-resident juveniles. During the summers of 2013–2014, we used anchored gill nets and trammel nets to sample juvenile Atlantic sturgeon throughout the Savannah River estuary. Ages of captured juveniles were determined using length-frequency histograms that were verified with fin ray cross sections from a subsample of the captured fish. Abundance of each juvenile age class was then estimated with Huggins closed-capture models in RMark. Our results showed that the Savannah River contained 528 (95% CI, 402–726) age-1 juveniles in 2013 and 616 (95% CI, 500–775) age-1 juveniles in 2014. These findings suggest that the Savannah River population is likely the 2^nd largest within the South Atlantic DPS.  Future estimates of juvenile abundance should help provide quantified information regarding population trends as well as identify key environmental variables affecting recruitment in the Savannah River system.

JAGS - WGSA Workshop Series

UPDATE: Here is the PowerPoint presentation from this workshop for your reference.

The next WGSA Workshop will be help on Wednesday (2/11) at 4:00 in the Dean's Conference Room. Paige Howell will lead us in an introduction to JAGS, a Bayesian software program. Please see a more detailed description below, and we hope you can join us!

Crash course in using JAGS through the R interface. Participants should have R (http://www.r-project.org/) installed on their computer as well as the rjags package and JAGS (http://mcmc-jags.sourceforge.net/) before coming. The workshop will briefly cover the basics of Bayesian inference using Markov Chain Monte Carlo simulation. Participants will have a chance to work through an exercise building a model with the JAGS language and executing their script in R. Past experience with R, maximum likelihood parameter estimation, and generalized linear models is useful but not required.

Files for the course:
JAGS crash course
tadpole data
Poisson regression