BC Groundfish Synopsis Reports

Generate reproducible data synopsis reports for over 100 species of British Columbia groundfish with standardized visualizations and statistical analyses.

Description

This skill helps you work with the `gfsynopsis` R package repository, which creates technical reports with standardized visualizations of fisheries data including catch statistics, survey maps, length/age compositions, and abundance indices. The reports follow Canadian Science Advisory Secretariat (CSAS) formatting standards.

Instructions

When working with this repository, follow these guidelines:

1. Understanding the Report Generation Pipeline

The report generation follows a multi-step pipeline:

1. **Data Loading** - Cached data objects stored in `report/data-cache-*/` directories

2. **Model Fitting** - Survey indices and CPUE models fitted using sdmTMB and other statistical packages

3. **Figure Generation** - Species-specific 2-page figure sets created via `make_pages()` function

4. **Report Compilation** - Bookdown reports compiled from R Markdown files

2. Building Reports

To generate synopsis reports:

Main report directories:

3. Key Data Processing Scripts

4. Package Structure

The repository follows standard R package conventions:

5. Configuration and Settings

6. Data Architecture

7. Key Dependencies

Be aware of these critical R packages:

8. Best Practices

Usage Examples

**Generate all figures and render main English report:**

```bash

Generate figures

Rscript report/make.R

Navigate to report directory and render

cd report/tech-report-main/

Rscript -e "csasdown::render()"

```

**Generate figures for specific species using parallel processing:**

```bash

./report/build_figures.sh

```

**Fit survey abundance index models:**

```bash

Rscript report/R/04-survey-index-standardization.R

```

Constraints