wham.Rmd

# State-space models revisited: Woods Hole Assessment Model (WHAM) {#wham}

As usual, course materials not in the github repository can be found in the course Google Drive [course-materials folder](https://drive.google.com/drive/folders/1Wt4fhAgCP92aBu_XSCQq50Xrkc-UVHnx?usp=sharing). Everything will of course be linked to here on the website.  

## 11/01, state-space population dynamics models {.unlisted .unnumbered}

Guest lecture from __Dr. Gregory Britten, MIT__  
(fully remote)  

[slide deck](https://docs.google.com/presentation/d/1U2I1NAjqBGxqqO0baNlmrikYvaAHbSF9wydiF-lHZrQ/edit?usp=share_link)  
[Materials](https://drive.google.com/drive/folders/1c1Yy5jD2-DMUu2H2qk4nIyoVbBNUMhIO)  

*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 {.unlisted .unnumbered}

Guest lecture from __Dr. Tim Miller, NOAA NEFSC__  

[slide deck](https://drive.google.com/file/d/1uvTm4guuzPEgYERWAzUxKmJwAwVVyUGI/view?usp=share_link)  

[R Markdown tutorial](https://drive.google.com/file/d/1HLeJQ3SGxcHVqTJwqqEQugesP1xN4Wdv/view?usp=share_link)  

*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.](https://doi.org/10.1016/j.fishres.2021.105967)  

*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](https://github.com/timjmiller/wham)  


## 11/08, Climate-linked stock assessment models {.unlisted .unnumbered}

Guest lecture from __Amanda Hart, UMassD-SMAST & GMRI__  

[Lecture slides](https://docs.google.com/presentation/d/1DCFof6nzsCnxXpSaoLb5p5jCE-Kjdk-B/edit?usp=share_link&ouid=100082783551785338508&rtpof=true&sd=true)  

[Supplemental reading - 2021 American Plaice Working Group Report](https://drive.google.com/file/d/1BodHCKG7OaIIfqsMkmm63bVfaqIGyDSG/view?usp=share_link)  


## Primary Reading {.unlisted .unnumbered}

[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.](https://doi.org/10.1016/j.fishres.2021.105967)