https://github.com/blue-matter/safmc-mse

Repository for the SAFMC MSE Process

https://github.com/blue-matter/safmc-mse

Repository

Repository for the SAFMC MSE Process

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# SAMSE





![](man/figures/logo.png)

## Introduction

The [South Atlantic Fishery Management Council](https://safmc.net/) (SAFMC) is working with [Blue Matter Science Ltd.](https://www.bluematterscience.com/) to conduct a Management Strategy Evaluation (MSE) to describe the expected outcomes of different management approaches for the Snapper-Grouper Fishery.

This `SAMSE` R package includes all the code to run the MSE analysis. `SAMSE` builds age-structured, spatial and multispecies, operating models (OMs) from the output of Beaufort Assessment Models (BAM). The OMs are projected under forwarded different management scenarios and performance statistics are used to compare the performance of different management approaches.

`SAMSE` uses the [openMSE](https:://openMSE.com) platform to build the OMs and conduct the closed-loop simulation testing.



## Installation

You can install the SAMSE from [GitHub](https://github.com/) with:

``` r
# install.packages("remotes")
remotes::install_github("Blue-Matter/SAFMC-MSE")
```

## MSE Technical Group Members

| Name              | Email                                                                        | Role                          |
|:-----------------------|:-----------------------|:-----------------------|
| Adrian Hordyk     | [adrian\@bluematterscience.com](mailto:adrian@bluematterscience.com){.email} | Lead MSE Analyst              |
| Quang Huynh       | [quang\@bluematterscience.com](mailto:quang@bluematterscience.com){.email}   | Supporting MSE Analyst        |
| Tom Carruthers    | [tom\@bluematterscience.com](mailto:tom@bluematterscience.com){.email}       | Supporting MSE Analyst        |
| Chip Collier      | [chip.collier\@safmc.net](mailto:chip.collier@safmc.net){.email}             | SAFMC Lead                    |
| Cassidy Peterson  | [cassidy.peterson\@noaa.gov](mailto:cassidy.peterson@noaa.gov){.email}       | MSE Specialist                |
| Erik Williams     | [erik.williams\@noaa.gov](mailto:erik.williams@noaa.gov){.email}             | Stock Assessment Specialist   |
| Christina Wiegand | [christina.wiegand\@safmc.net](mailto:christina.wiegand@safmc.net){.email}   | Social Scientist              |
| Scott Crosson     | [scott.crosson\@noaa.gov](mailto:scott.crosson@noaa.gov){.email}             | Economist                     |
| Mike Larkin       | [michael.larkin\@noaa.gov](mailto:michael.larkin@noaa.gov){.email}           | Data Analyst                  |
| Kai Lorenzen      | [klorenzen\@ufl.edu](mailto:klorenzen@ufl.edu){.email}                       | Meeting Moderator/Facilitator |
| Mike Schmidtke    | [mike.schmidtke\@safmc.net](mailto:mike.schmidtke@safmc.net){.email}         | SAFMC Fishery Scientist       |
| Judd Curtis       | [judd.curtis\@safmc.net](mailto:judd.curtis@safmc.net){.email}               | SAFMC Fishery Scientist       |
| Allie Iberle      | [allie.iberle\@safmc.net](mailto:allie.iberle@safmc.net){.email}             | SAFMC Fishery Scientist       |

## MSE Process Documents

- [MSE Technical Specifications](https://safmc-mse.bluematterscience.com/resources/TS/TS.html): document describing the technical details of the MSE framework, including the methodology and assumptions for creating the operating models. 
- [Building Base Case Operating Model](https://safmc-mse.bluematterscience.com/articles/Building-Base-Case-Operating-Models.html): article providing a description and reproducible code for generating the Base Case Operating Models.
- [SAFMC MSE Results App](https://shiny.bluematterscience.com/app/samse): An online App designed to interactively explore the MSE Results

## Background Documents

### Assessment Reports
- [SEDAR 71 South Atlantic Gag](resources/SEDAR_Reports/sedar-71-stock-assessment-report-south-atlantic-gag.pdf)
- [SEDAR 73 South Atlantic Red Snapper](resources/SEDAR_Reports/sedar-73-stock-assessment-report-south-atlantic-red-snapper.pdf)
- [SEDAR 76 South Atlantic Red Snapper](resources/SEDAR_Reports/sedar-76-stock-assessment-report-south-atlantic-black-sea-bass.pdf)

## Additional Resources and Material

-   [openMSE](https://openmse.com/): the MSE framework used to conduct the closed-loop simulation testing.

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