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---
title: "Introduction to Management Strategy Evaluation"
author: "Gavin Fay"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
description: "This is a CINAR training workshop held remotely 10-14 January 2022"
---
# Welcome {#welcome}
_Introduction to Management Strategy Evaluation to support strategic decision-making for fisheries management_: Hello! This is a course taught by Dr. Gavin Fay for CINAR: Jan 10-14 2022.
__Description__: This training workshop provides fisheries scientists with instruction and hands-on practical modeling experience in an introduction to Management Strategy Evaluation (MSE), for applications to Northeast and Mid-Atlantic managed stocks and key concerns, and participation in MSE working groups and technical committees. MSE is a well-recognized approach for strategic decision-making in fisheries management, providing methods to compare among policy options and assess their robustness in meeting a range of management objectives.
The objectives of the workshop are to: 1) Provide an overview of the MSE process and components of an MSE, and 2) demonstrate through applied examples and modeling exercises on the components of closed loop simulation analyses that form the basis of the analytical aspects of an MSE.
Modeling exercises and case studies will emphasize different aspects and features of MSEs, and a range of examples will emulate features of the stock dynamics and fisheries managed by the NEFMC, MAFMC, and ASMFC. A key part of the workshop will be small group projects applying a simple desktop MSE to example case studies for a small problem scope. These will be developed through the workshop, with presentations to other groups on the last day of the workshop. See questions on suggested examples below.
The workshop will consist of synchronous webinar sessions, with active learning opportunities through discussions and in-class modeling exercises, a set of short evening readings, and additional optional homework to further develop the case studies explored.
The primary focus of the workshop will be on the technical analysis components of MSEs and the interpretation and visualization of results, but the role of stakeholder engagement in MSE processes for co-developing objectives, policy alternatives, and performance metrics will also be overviewed.
This website (built in R!) provides access to the workshop materials and will be updated during the workshop as we progress (and adapt).
**This website**: <https://gavinfay.github.io/cinar-mse/>
**GitHub repo**: <https://github.com/gavinfay/cinar-mse>
---
**About the instructor**
[Gavin Fay](https://thefaylab.com) (he/him) is an Associate Professor of Fisheries Oceanography at the University of Massachusetts Dartmouth's School for Marine Science and Technology, based in New Bedford, MA. He is a 2020-2022 CINAR Fellow in Quantitative Fisheries & Ecosystem Science, funded through the NOAA Northeast Fisheries Science Center and NOAA Fisheries' Quantitative Ecology & Socioeconomics Training program (QUEST). This workshop is part of Dr. Fay's CINAR Fellowship activities.
[Email](mailto:[email protected])
[Twitter](https://twitter.com/gavin_fay)
---
## Agenda {.unnumbered}
_(subject to change)_
|Day|Time|Topic|
|:--|:----|:---------|
| M | 10-10:30 | [Intro, Workshop overview](#intro) |
| M | 10:30-12 | [What is MSE? (lecture and MSE game)](#intro) |
| M | 1-3 | [My first MSE (breakout R intro exercise)](#first-mse) |
| M | 3:30-4:30 | [code-through of first mse (R: intro exercise)](#first-mse) |
| M | 4:30 - 5 | [Case studies discussion](#case-studies) |
| T | 9-9:30 | Reading discussion |
| T | 9:30-10:30 | [Objectives & Performance metrics (lecture)](#objectives) |
| T | 11-12 | [Case studies: developing objectives & candidate strategies for examples (breakout exercise)](#case-studies) |
| T | 1-2 | [Including the ecosystem in MSEs (discussion)](#environment) |
| T | 2-3 | [designing operating models (lecture)](#op-mods) |
| T | 3:30-5 | [coding & implementing OMs (R lab breakouts)](#coding-oms) |
| W | 9-9:30 | Reading discussion
| W | 9:30 -10:30 | [Code-through of day 2 exercise](#objectives) |
| W | 11-12 | [Case study review. Relevant OM & HCR needs.](#project-needs) |
| W | 1-2:30 | [selecting management strategies (lecture, R: comparing HCRs)](#management-strategies) |
| W | 3-4 | breakout group coding on case study projects |
| W | 4-5 | [Presenting results to managers (lecture)](#communication) |
| Th | 9-9:30 | Reading discussion
| Th | 9:30-10:15 | [Implementation error (lecture)](#implementation) |
| Th | 10:15-12 | Case study project work time |
| Th | 1-1:45 | Atlantic bluefin tuna case study (lecture/discussion) |
| Th | 1:45-3:30 | Case study project work time |
| Th | 3:30-5 | [multispecies MSEs (lecture, R exercise)](#ecosystem-mse) |
| F | 9-10 | [OMs & EMs revisited](#oms-revisited), [Additional MSE topics (lecture)](#grab-bag) |
| F | 10:30-12 | Case study project summaries, Workshop review |
[Breakout Group Assignments](https://docs.google.com/spreadsheets/d/1RlRCivOBiYB7phizz4YKWoDLTE5WbdSMnL29_3oIb-c/edit?usp=sharing)
## Pre-workshop preparations (15 minutes) {.unnumbered}
The workshop will be run via Zoom, and we will be using a GoogleDoc for shared note taking and interaction during the sessions. Breakout sessions and analytical components will be conducted using R.
For R, there are two options: either have R & RStudio downloaded on your machine, or use a RStudio Cloud project created for this workshop (recommended).
Why RStudio Cloud? We want to maximize time during our workshop for learning, and not on tech support. Using a standard way of interacting with the course material makes this easier, and avoids the hassles of multiple installation types, versions of R, etc. However, you may wish to set up R and RStudio on your local machine, so information about required packages will be posted below.
### RStudio Cloud {.unnumbered}
Before the workshop, please visit [Rstudio Cloud](https://rstudio.cloud) and create a free account.
Free accounts give limited usage, but are more than enough for these workshops.
Instructions for how to navigate to our RStudio Cloud project and set up the project so you can work on the exercises in your own web browser can be found here.
[RStudio Cloud set up guide & instructions](https://github.com/gavinfay/cinar-mse/issues/1)
### R & RStudio on own machine {.unnumbered}
**Download and install R and RStudio**
- R: <https://cloud.r-project.org/>
- RStudio: <http://www.rstudio.com/download>
- Follow your operating system's normal installation process
**Getting the workshop materials to your computer**
You can create a R Studio project from the github repository for the workshop.
[RStudio project set up guide](https://github.com/gavinfay/cinar-mse/issues/2)
**R Packages used**
If not using the RStudio Cloud project, we will be using the following R packages and you can install them on your local machine ahead of time by running the below code in the R console (copy & paste).
```{r eval=FALSE}
pkgs_to_use <- c("tidyverse",
"ggdist",
"palmerpenguins",
"furrr",
"MASS",
"janitor",
"skimr",
"Hmisc",
"mvtnorm",
"bookdown",
"RcppRoll")
install.packages(setdiff(pkgs_to_use, rownames(installed.packages())))
```
## Code of Conduct {.unnumbered}
These workshops follow the [Fay Lab code of conduct:](https://thefaylab.github.io/lab-manual/code)
## Licensing {.unnumbered}
All materials are released with [Creative Commons Attribution Share Alike 4.0 International](LICENSE.md) license.
## Acknowledgements {.unnumbered}
This website is built with [bookdown](https://bookdown.org/), and the lovely icons by [icons8](http://icons8.com/). The course website design was based on both the [R for Excel Users](https://rstudio-conf-2020.github.io/r-for-excel/) course by Julie Lowndes & Allison Horst, and the [Data Science in a Box](https://datasciencebox.org/) course by Mine Çetinkaya-Rundel, and on a course structure developed by Gavin Fay for ASMFC in 2021. All errors are purely by Gavin. Content in the course includes materials originally developed by [André Punt](https://fish.uw.edu/faculty/andre-punt/). Lectures and exercises that include material from André are noted on the title slide or at the top of scripts/Rmarkdowns. Again, all errors by Gavin. Some additional slide content courtesy of Jonathan Cummings, Jonathan Deroba, Amanda Hart, Lisa Kerr, Mackenzie Mazur, Molly Morse, Sam Truesdell, and Ashley Weston.