Author Archive

QFC presence at AFS

The QFC had a large presence at this year’s AFS meeting with 7 members attending. We were active participants giving three talks and teaching a workshop. First Jim, Lisa, Travis and Yang taught the Introduction to Programming in R for Fisheries Scientists workshop which had 15 participants. One participant enjoyed the workshop enough to sign up for our full online course.

Jim spoke about experiences in implementing temporally varying parameters in real assessments and Travis spoke about simultaneous analysis of genetic and length data to estimate changes in year-class strength of Lake Michigan Lake Sturgeon in the Practical Applications of Sturgeon Research symposium. Yang gave a talk in the Next Generation of Fish Stock Assessments symposium about the influence of stock assessment frequency on achievement of fishery management objectives.

It was also nice to see several QFC alumni at the meeting including Mike Wilberg, Aaron Berger, Matt Catalano, Carson Prichard and Gretchen Hansen.

The QFC is a featured research group!

The QFC is a featured research group on the High Performance Computing Center at Michigan State University. The HPCC is an easy-to-use high performance computing that enable larger, broader and more complex computation than ever before—work that could have taken months or years now can be done in hours or days. Read more about how we use the HPCC for our research projects.

Resized QFC Image

Visitors at the QFC

The QFC welcomes visitors this summer. Rahman Patimar is on sabbatical leave from Gonbad Kavoos University in Iran, where he is an associate professor. At his home institution he has done teaching on fish population dynamics and ichthyology and research on a variety of fish populations, in particular Cyprind species of the Caspian Sea. Rahman will be at the QFC through the spring of 2015 and is taking time during his visit to learn new methods of data analysis and modeling of fish populations. He hopes to apply what he is learning to example data sets from North America.
We also welcome two master’s students from Shanghai Ocean University. These students are among a group of students visiting Michigan State University for 2 weeks and have a special interest in quantitative methods. They will spend time working through our online Introduction to R Course as well as collaborating with our knowledgeable staff.
The QFC will be seeing many new visitors in the future with our newly launched visiting scientist and secondment program. Participants will have an opportunity to spend time at the QFC, working with QFC staff and learning quantitative fisheries methods. You can learn more about the programs here

R Programming Workshop At AFS and Article Summary

Jim Bence and Travis Brenden from the QFC will be teaching an AFS continuing education course at the American Fisheries Society annual meeting on Sunday August 17, 8am-5pm. The early registration deadline is June 20. If you are interested we encourage you to sign up by the deadline to help avoid the chance of the course being cancelled due to low enrollment! The cost of the course is $150 for AFS members, $200 for non-members, $100 for AFS student members and $130 for non-AFS students. In addition the QFC offers a more extensive online R course and will offer discounts to those who take the AFS R course and then sign up for the online course in the next year. For more information on the AFS R course see and for more information on our online R course see

Also, check out this article summary on work by QFC’s Iyob Tsehaye, Michael L. Jones, Travis O. Brenden, James R. Bence while you are are registering!  Boom and Bust in Lake Michigan

Lisa Peterson successfully defended her MS thesis!

On May 1, Lisa Peterson successfully defended her MS thesis, titled Investigating Assumptions Made in the Assessment of Lake Erie Yellow Perch. For the first part of Lisa’s thesis research, she investigated the assumption that there was no movement of yellow perch between the four management units in Lake Erie. She used a statistical catch-at-age model that assumed movement between two of the management units to evaluate the effect this assumption had on the results of the stock assessment (e.g. abundance estimates, catchability). Lisa’s second chapter of her thesis focused on a catch-rate standardization for the Ohio trawl survey data that is used in the stock assessment as an index of yellow perch abundance. She developed a model that took into account different environmental factors to extract a standardized index. These factors included a wind component that incorporated both wind speed and direction, which are not commonly used in catch-rate standardizations. She then compared the standardized index of yellow perch with the non-standardized index to investigate the effect these factors have on catch rates in Lake Erie. Lisa has some edits to make to her thesis before she can submit a final copy to the Michigan State University Graduate School, but these should be completed in early summer. Lisa is continuing on in the Quantitative Fisheries Center as a PhD student and is in the beginning stages of her project. Congratulations Lisa!!!
Read more about her work from the Lake Erie Committee

QFC Computing Resources – 1Q 2014

During the first quarter of 2014 we made two important changes to the QFC computing environment which impacted our computing resource meters. We replaced two older processors running Windows XP with new equipment and Windows 7. Microsoft dropped support of Windows XP in April 2014 leaving users vulnerable to security problems. With the exception of some general use computers, all processors at the QFC are now running fully supported operating systems. In mid-March, we migrated from our hardy but aging server to a new server. The existing QFC web site and FTP hosts were successfully rebuilt on the new server with minimal disruption to online service. The replacement of these three processors by newer equipment increased the total computing resources at the QFC ( The most significant increase occurred in our hard drive capacity, which increased by 50%, to allow us to keep most of our historical data files online and readily available.

1Q 2014 jpg

QFC Co-director Mike Jones traveled to Rome

QFC Co-director Mike Jones traveled to Rome, Italy in early March to attend the 2nd International Conference on Fishery Dependent Information. Aside from making the most of his first ever visit to Rome (what an amazing city!), Mike presented on the QFC work with the Lake Erie Percid Management Advisory Group (LEPMAG). One of the primary themes of the conference was developing ways to improve stakeholder involvement in the process of developing fishery harvest policy. There were many other presentations on stakeholder involvement in fishery management – there is a very high level of interest in this in Europe – and Mike came away from the meeting feeling very good about our accomplishments with LEPMAG relative to the global experience in engaged harvest policy analysis. It was really valuable to meet “kindred spirits” from Europe, Australia, and New Zealand, and learn about their experiences with similar challenges. The proceedings of the conference are expected to be published in a special issue of the ICES Journal of Marine Science.

Vandergoot Successfully Defends Dissertation

On March 14, Chris Vandergoot successfully defended his PhD dissertation, bringing him one step closer to officially becoming Dr. Vandergoot. The title of his dissertation is Estimation of Regional Mortality Rates for Lake Erie Walleye Sander vitreus Using Spatial Tag-Recovery Modeling. As part of Chris’ dissertation research, he analyzed recoveries from a Lake Erie walleye jaw-tagging study that started in 1990 and ran for nearly 20 years. In total, more than 100 thousand walleyes were tagged during this study. Chris used recoveries from the study to estimate regionally-varying demographic parameters for the Lake Erie walleye population that can be of great use to fishery managers (e.g., movement rates, mortality components). Chris also conducted simulations to explore how features of tagging study designs affect our ability to accurately and precisely predict parameters of interest with an eye towards providing recommendation for future tagging studies that might be conducted on the lake. Chris has some minor edits to make to his dissertation before he can submit a final copy to the Michigan State University Graduate School; Chris is diligently working towards completing those edits. While pursuing his PhD, Chris has also been full-time employee of the Ohio Department of Natural Resources Division of Wildlife at the Sandusky Fisheries Station. Chris was recently promoted to Fisheries Biology Supervisor for the research station, so he is very much relieved to have his studies wrapped up. Congratulations Chris!!!

Making the “jump” to a new server

The QFC will be migrating online services to a new server from March 14-16, 2014. Services that will be impacted during this time include the QFC web site, ftp, and listserv functions. The move to the new server will necessitate physically migrating ftp files. Please plan to complete all ftp transfers before midnight Thursday March 13th. Any ftp transfers occurring after this time and before we complete the migration, may not be copied to the new server. Web site and listserv services should experience only minimal disruption and may be inaccessible for short periods of time during the transition. We expect normal operations to resume on Monday March 17th. If you experience any difficulties after this time, please contact us at 517-355-0126.
Old to New Server

QFC Shuffle

For the past few months we’ve been busy doing housecleaning at the QFC. Our computing resources – workstations, printers, fax, and copier – were located in various places around the QFC, including our conference room. An external review of the QFC last summer noted that items for general use should not be in the conference room. We also wanted to logically arrange items, for instance, move all printers to one location. As we reorganized the equipment, we also installed two additional electrical circuits to partition mission critical equipment on separate circuits from general use equipment. We are pleased to show you the results of all our shuffling. Our conference room is more spacious, so meetings don’t feel so cramped and our common use area comfortably supports both the shared computing resources and our lunch area.

Conference Room

Conference Room

Common Area

Common Area



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