https://github.com/pbs-assess/dogfish-inside

Stock Assessment for Inside Dogfish Stock in British Columbia
https://github.com/pbs-assess/dogfish-inside

Last synced: 18 days ago
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Stock Assessment for Inside Dogfish Stock in British Columbia

• Host: GitHub
• URL: https://github.com/pbs-assess/dogfish-inside
• Owner: pbs-assess
• Created: 2024-01-22T16:41:39.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-11-08T22:01:41.000Z (3 months ago)
• Last Synced: 2024-11-08T22:32:07.921Z (3 months ago)
• Language: R
• Homepage:
• Size: 4.8 MB
• Stars: 0
• Watchers: 14
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.Rmd

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README

        
---

output: github_document

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE)

```

# Inside Dogfish Stock Assessment for British Columbia

## Install dependencies

### GitHub R packages

```{r github-packages, eval=FALSE}

# install.packages("remotes")

remotes::install_github("pbs-assess/gfdata")

remotes::install_github("pbs-assess/gfplot")

remotes::install_github("luke-a-rogers/ssio")

remotes::install_github("r4ss/r4ss")

remotes::install_github("Cole-Monnahan-NOAA/adnuts")

remotes::install_github("PIFSCstockassessments/ss3diags")

```

### Stock Synthesis 3.30

- Download the latest release of [Stock Synthesis 3.30](https://github.com/nmfs-ost/ss3-source-code?tab=readme-ov-file)

- Confirm that the ss3 executable is available in the R `$PATH`, for example using `r4ss::check_exe()`

## Fleets

Fleets are defined by a combination of `gear` type (e.g. "Hook and line") and 

`type` (e.g. "landings"). Because fleet definitions may differ between

models, data files for catch (catch.rds), indexes (index.rds), and lengths 

(length.rds) are stored (in data/ss3/) with `gear` and `type` columns,

to allow the analyst to define fleets specific to each model fit (typically in

ss3/xxx/00-fleets.R) in combination with the R package ssio (under development).

## Project status

- [x] Preliminary data uploaded and formatted

- [x] Simplified model structure adapted from dogfish-assess/ repo

- [x] Trial ss3 model in ss3/T00/ runs on 8 fleets

## Next steps

- [ ] Iterate trial model fits in ss3/T00/ to explore base model options

- [ ] Develop base model in ss3/A00/ using ss3/T00/ workflow

- [ ] Develop additional (sensitivity) model fits