README

Stephanie Peacock 2024-May-07

state-of-salmon

Overview

This repo contains code and data that informs the Pacific Salmon Foundation’s State of Salmon Report.

Files

• code contains R code for data compiltation and analysis:
  • 1_regions-expansions.R expands spawner abundance from stream-level spawner surveys to regional aggregate abundance.
  • 2_compile-regional-data.R compiles regional estimates of spawners and returns from various sources in data/, or uses the expanded spawner abundances from 1. where regional data were not available, and smooths these time series using a geometric running mean over the generation length for the species/region. Outputs the raw and smoothed time series as output/sps-data.csv.
  • 3_calc-metrics.R reads in output/sps-data.csv and calculates the current status and trends reported on in the State of Salmon report.
  • other supporting code in colours.R, expansion-functions.R, and functions.R are sourced in the above files and contain functions for expansion, smoothing, and plotting output.
• data has source data sets used in 2_compile-regional-data.R.
• output contains processed data and summaries that are usually produced by R code in code and used in plotting.
• docs contains Technical Documentation on the methods - see https://salmonwatersheds.github.io/state-of-salmon/

Acknowledgements

Code here is written by Steph Peacock and Eric Hertz. PSF’s State of Salmon reporting is led by Eileen Jones and funded by the Pacific Salmon Foundation.

More information

• Technical Documentation of the data sources and approach can be found at https://salmonwatersheds.github.io/state-of-salmon/.
• Output data sets provided here in output are available through the Salmon Watershed Program’s Data Library with associated metdata and citation information.
• If you have questions or would like more information, contact Steph Peacock speacock@psf.ca.