https://github.com/pbs-assess/gfmpa

Analysis of closed areas impact on survey indices
https://github.com/pbs-assess/gfmpa

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Analysis of closed areas impact on survey indices

• Host: GitHub
• URL: https://github.com/pbs-assess/gfmpa
• Owner: pbs-assess
• Created: 2021-08-18T23:34:46.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-02-08T02:09:37.000Z (11 months ago)
• Last Synced: 2024-11-10T13:28:27.728Z (2 months ago)
• Language: R
• Homepage:
• Size: 25.6 MB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

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README

        
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10633228.svg)](https://doi.org/10.5281/zenodo.10633228)

## Impacts on population indices if scientific surveys are excluded from marine protected areas

Code for an analysis of impacts on population indices if scientific surveys are

excluded from MPAs. The analysis focuses on groundfish and the Northern Shelf

Bioregion MPA network off the west coast of Canada.

### Citation:

Anderson, S.C., P.A. English, K.S.P. Gale, D.R. Haggarty, C.K. Robb, E.M. Rubidge,

and P.L. Thompson. Impacts on population indices if scientific surveys are

excluded from marine protected areas. ICES Journal of Marine Science.

https://doi.org/10.1093/icesjms/fsae009

### Folders:

- `analysis`: code to run the analyses

- `data-generated`: data that have been manipulated and cached

- `data-raw`: raw data; mostly kept locally and not in version control due to size

- `figs`: generated figures

- `text`: manuscript text; copied from an Overleaf repository (do not edit here)

### Analysis instructions:

To recreate the analyses, the R files in `analysis` need to be run in numerical

sequence. The first file (`01-load-data.R`) does not need to be run since all

data generated by that file have been cached and committed to this Git

repository. Some analyses take considerable time to run (hours to a day

depending on the computer). In particular, `02-fit-geostat.R` (which fits all

the spatiotemporal models) and to a lesser degree `05-power.R` (which runs a

power analysis with spatiotemporal models) will be slow.

### R Packages:

All R packages used should be available on CRAN with the following exceptions:

```r

install.packages("remotes")

remotes::install_github("seananderson/ggsidekick")

remotes::install_github("ropensci/rnaturalearthhires")

# available on CRAN, but suggest using the latest development version:

remotes::install_github("pbs-assess/sdmTMB", dependencies = TRUE)

```