Trend_Analysis/README.Rmd at main · CCAMLR-Science/Trend_Analysis · GitHub

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---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit the .Rmd file then knit it -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# Trend analysis

Latest reports: [WG-SAM-2024/12](https://meetings.ccamlr.org/en/wg-sam-2024/12) and [WG-FSA-IMAF-2024/12](https://meetings.ccamlr.org/en/wg-fsa-imaf-2024/12).

## Annual updates

Before starting an update, make sure all changes have been pushed and that the current branch has been merged with the main. Then create a new branch in Rstudio, one per meeting, *e.g.* SAM23 then FSA23 and work on these branches separately.


There are several things to update annually. Some things might just need to be reviewed, others might need updating.

1. Review/update the shapefile of buffered Research Blocks.

In the subfolder *~/Data*, the shapefile "BufferedRBs" contains the RBs after buffering (+5km). It is generated using *BufferRBs.R* which also produces a plot ("BufferedRBs.png") to look at the buffers, which get a bit special when RBs have shared boundaries (shown in blue/orange on the plot - those in green do not share boundaries with other RBs). If a new RB has been created, or an existing RB has been modified or removed, you will need to update the shapefile.

2. Review/update the shapefile of Reference Areas (HIMI and RSR_Open).

In the subfolder *~/Data*, the shapefiles "RefAreas" and "RefAreasLL" contain the reference areas. These are generated using *RefArea_Shp_Maker.R*. "RefAreasLL" is the unprojected version, used to compute fishable area within the script *FishableArea.R* (see [WG-FSA-2021/06](https://www.ccamlr.org/en/wg-fsa-2021/06) for details).

3. Review/update Fishable areas.

In the subfolder *~/Data*, the csv file "FishableAreaYYYY.csv" contains the fishable area of RBs and Reference Areas. It is generated using *FishableArea.R*. This needs to be updated when those areas are updated and/or when the GEBCO bathymetry is updated. If fishable areas have been updated, the effect of the update must be analyzed (and run *CompareGEBCOs.R*).

4. Review/update Map and Area Thumbnails.

In the subfolder *~/Data*, the images *Map_TrendAnalysis.png*, *Area48.png*, *Area58.png* and *Area88.png* are generated using *Map_and_AreaThumbnails.R*. These images are used in the report and trend plots, and may be updated in that script, if needed.

5. Update past catch limits.

Every year new catch limits are agreed upon. Use the *GetCLs* script (only once a year), but always double check with the SC table of catch limits. If a new RB is created, add a row for it.

6. Review/update vulnerable biomass estimates

Once stock assessments in the Reference Areas have been agreed by the Commission, contact the authors (might as well do it during FSA) and ask them for these values. They go in the script *00_RunAnalysis.R*, under "#Set biomass and CV for Reference Areas". Record these values also in *01_LoadData.R* for posterity.

7. Review/update the list of RBs that require catch advice (wait until the 1 June notification deadline)

Update list (*RBsCAdv* in *00_RunAnalysis.R* and in *Map_and_AreaThumbnails.R*) based on the ASDs that have notifications (https://www.ccamlr.org/fishery-notifications/notified/nesummary or https://www.ccamlr.org/fishery-notifications/notified/research).


## How to run the analysis

Simply run "00_RunAnalysis.R", it will source all other scripts.