Link to original announcement

Feb 8-12th 2016 9AM - 5PM each day, breaks occasionally

Room 106 School of Aquatic and Fisheries Sciences 1122 NE Boat St, Seattle, WA 98105

Template Model Builder (TMB) advances practices developed in ADMB by improving ways to deal with random effects and a wider range of contributed libraries. This introductory workshop will help familiarize participants with approaches to model development in TMB. Contrasts with ADMB will be covered, though participants are not required to be proficient in ADMB. Participants are assumed to have a background in applied statistics and statistical computing. Specifically, some experience fitting nonlinear models to data (in stock assessment or elsewhere) and basic programming skills. Arni Magnusson and Jim Thorson will guide the workshop; participation is be open to NOAA staff who are able to attend, UW students, and other interested scientists depending on space availability. Workshop facilitation by Jim Ianelli and any other volunteers. UW Spring Quarter 4-credit course: “Spatio-temporal models for ecologists” will use TMB extensively.

###Activities

1. Overview of different ways to install and update TMB, incl. GitHub repository access
2. Overview of TMB workflow and alternative working environments
3. Demonstrations and exercises, starting with simple models and gradually adding complexity
4. Statistical techniques to evaluate uncertainty and the use of random effects, as well as debugging
5. User-specific applications
6. Identify areas where enhancements to TMB documentation and training are needed

Dates : February 8-12, 2016

Contact : Jim.Ianelli@noaa.gov for registration and questions.

The general structure of the workshop is that mornings will be lectures and demonstrations (how to build TMB models), while afternoons will be explorations of different software components (how to contribute to TMB development). Throughout the workshop, we will get an overview of the existing TMB documentation and identify where enhancements are needed.

People who are unable to attend the whole workshop are encouraged to drop in whenever they can.

The afternoons will not follow a rigid structure, so participants can focus on a particular software component in their area of expertise and interest. In particular, from Wednesday afternoon it is planned that users will be able to implement their model of interest for their own research.

Below are some case studies that might be of interest for different groups (please consider submitting your topic of interest!)

• Random effects for estimating future fishery weights at age (Jim I.)
• Time series modeling (building from examples)

1. Please join my meeting. https://global.gotomeeting.com/join/534027645

2. Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

• Dial +1 (224) 501-3312

• Access Code: 534-027-645

• Audio PIN: Shown after joining the meeting

• Meeting ID: 534-027-645

Arni, did you have an updated sense of how to structure the workshop given then exchanges we had yesterday? I think we had settled on a morning-lecture, afternoon-workshop format with 2 days devoted to the geostatistical index standardization tool and spatio-temporal models. do you have ideas for teh remaining 3 days?

Below is a list provided from the core developer (Kasper Kristiansen) on ways the workshop may contribute to the TMB work.

1. Documentation. Some example tasks:

   • Create text versions of Latex displaymath formulas (so that formulas show up nicely not only in the pdf docs).
   • Doxygen documentation clean up.
   • Roxygen documentation clean up.

2. More streamlined testing workflow. Could be something like travis (Ben Bolker set it up for glmmTMB). But travis might not be sufficient. The ideal setup should run all tests on all combinations of

   • Operating system
   • With/without precompile
   • CRAN version / not CRAN version It should further be able to detect performance regressions - both in terms of runtime, compilation time and memory usage. (BTW we should keep an eye on https://github.com/r-hub/proposal )

3. Make debugging work on windows.

4. Make good consistent test scripts of e.g. the TMB array class, matrices etc. Purpose is to demonstrate syntax and test for correctness. There are some tests in "adcomp/tmb_syntax" but it needs improvement.

SEFSC Beaufort lab

NEFSC Legault/Brooks/Shank

(D)UMASS Gavin Fay, Megan Winton (mwinton@umassd.edu)

NWFSC / Newport lab

SWFSC (Huihua, 5-10 people)