Chapter 9 State-space models revisited: Woods Hole Assessment Model (WHAM)

As usual, course materials not in the github repository can be found in the course Google Drive course-materials folder. Everything will of course be linked to here on the website.

11/01, state-space population dynamics models

Guest lecture from Dr. Gregory Britten, MIT
(fully remote)

slide deck
Materials

Software:
The materials require {rstan} be installed. The course RStudio Cloud machine already has this installed. For those using wanting to run things locally, please install {rstan} ahead of time. e.g.
install.packages('rstan')

11/03, Woods Hole Assessment Model

Guest lecture from Dr. Tim Miller, NOAA NEFSC

slide deck

R Markdown tutorial

Reading:
Stock, B.C. and Miller, T.J., 2021. The Woods Hole Assessment Model (WHAM): a general state-space assessment framework that incorporates time-and age-varying processes via random effects and links to environmental covariates. Fisheries Research, 240, p.105967.

Software:
The course RStudio Cloud machine has WHAM installed. For those using wanting to run things locally, please ensure you have the ‘devel’ branch of WHAN installed. e.g.
devtools::install_github("timjmiller/wham", dependencies=TRUE, ref="devel")

More installation istructions and information about wham, see the github repository:
https://github.com/timjmiller/wham

11/08, Climate-linked stock assessment models

Guest lecture from Amanda Hart, UMassD-SMAST & GMRI

Lecture slides

Supplemental reading - 2021 American Plaice Working Group Report