galuardi / feb2016

UW Workshop

Introductory TMB (and ADMB comparison) workshop

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

Summary

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 : [email protected] for registration and questions.

Format

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.

Schedule

Day	AM/PM	Activity
Mon	am	Intro to TMB, building simple models
Mon	pm	Closer look at installation, GitHub, RStudio/Emacs/other
Tue	am	Working with parameters, nonlinear models
Tue	pm	Anatomy of the TMB package, objects, and overall design, group projects (breakouts?)
Tue (Fat)	ppm	Some sort of Mardi gras celebration...
Wed	am	Group project updates, Stock assessment models, debugging uncertainty estimates, MCMC developments (Cole)
Wed	pm	Debugging in TMB, contributing to the development, working on projects from groups
Thu	am	Group project updates, Random effects, geostatistical methods
Thu	pm	Related C++ libraries and R packages, CppAD, glmmTMB
Fri	am	Group project updates, Geostatistical and spatio-temporal models continued
Fri	pm	TBD (one degree of freedom)

Topics to consider for breakout groups

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)

Remote access

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 [phone]

• 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?

TMB Improvement efforts

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.

Participants

name	email	notes	N
Arni Magnusson	[email protected]	Hafro, Instructor!	1
Jim Thorson	[email protected]	NOAA, Instructor!	2
Jim Ianelli	[email protected]	NOAA	3
Kirstin Holsman	[email protected]	NOAA	4
Martin Dorn	[email protected]	NOAA, limited experience	5
Steve Martell	[email protected]	SS, Mac fanboy	6
Lee Qi	[email protected]	UW	7
Teresa A’mar	[email protected]	NOAA Off of Sci and Tech.	8
Gwladys Lambert	[email protected]	NOAA Post doc	9
Johnoel Ancheta	[email protected]	Univ of Hawaii, ADMB dude	10
Felipe Carvalho	[email protected]	JIMAR/NOAA	11
Yi-Jay Chang	[email protected]	JIMAR	12
Marc Nadon	[email protected]	JIMAR	13
Jessica Hale	[email protected]	UW	14
Paul Spencer	[email protected]	NOAA	15
Anne Hollowed	[email protected]	NOAA First day or 2	16
Marie Ferguson	[email protected]	NOAA	17
Andre Punt	[email protected]	UW	18
Brandon Chasco	[email protected]	UW/OSU	19
Jin Gao	[email protected]		20
Cole Monnahan	[email protected]		21
Bill Clark			22
Kelli Johnson	[email protected]		23
Allan Hicks	[email protected]		24
Noble Hendrix			25
Elizabeth Phillips	[email protected]		26

Remote access participants

SEFSC Beaufort lab

NEFSC Legault/Brooks/Shank

(D)UMASS Gavin Fay, Megan Winton ([email protected])

NWFSC / Newport lab

SWFSC (Huihua, 5-10 people)