README

Stephanie Peacock 06/09/2022

Testing for broad-scale relationships between freshwater habitat pressure indicators and Pacific salmon population trends

This repository contains code and data associated with an analysis to quantify the relationships between population status of Pacific salmon and habitat indicators. The project is a collaboration between DFO and the Pacific Salmon Foundation, building on the PSF’s recently updated Pacific Salmon Explorer and associated datasets.

This work has been published in the journal Ecological Indicators and is available open-access from https://www.sciencedirect.com/science/article/pii/S1470160X23000778.

Contents of this repo

Data

Contains most datasets in .csv format that are read in by code/dataCompilationNuSEDS_CU.R to compile a single dataset of population trends, habitat pressure, and other explanatory variables.

Population data were too large to upload to GitHub but can be downloaded at the following links:

• NuSEDS spawner estimates for each population and year, including data quality Estimate Classification Types are available here.

• Conservation_Unit_Data.csv, which organizes NuSEDS data by Conservation Units, is available here. (Note that this dataset does not include some of the fields in the above NuSEDS file, hence the need to import both.)

NuSEDS is currently undergoing some restructuring and we cannot guarantee that the format of the above data will be compatible with the code in this repo. Email us at the address below if you’d like the exact files used in our analysis.

The habitat pressure data are also publicly available from the Salmon Data Library, as “spatial datasets” separated by pressure indicator and region.

Code

Files for compiling and checking data

• dataCompilationNuSEDS_CU.R: imports NuSEDS data and several other sources described in the paper (provided in data/) to yield a filtered dataset of trends in spawner abundance per population and habitat pressure values associated with spawning watersheds of those populations. The “NuSEDS_CU” part refers to the NuSEDS data by CU that were used in this compilation.

• functions.R: contains several basic functions used repeatedly in data compilation.

Files for fitting Bayesian linear model in JAGS and visualizing results

• fitting.R: Code for fitting the model above to the population/habitat data compiled by dataCompilationNuSEDS_CU.R using JAGS and rjags. Note that this code involves parallel computation.

• loadPopData.R: Called by fitting.R and lookingAtOutput.R to import the population/habitat data and create additional variables for factor levels, etc.

• loadResults.R: Called by lookingAtOutput.R to load MCMC output of model fitting and organize parameter output in arrays.

• lookingAtOutput.R: Code for plotting the results of the model object from fitting.R and producing figures in the report.

• threatened.R: Code that takes the model object from fitting.R and samples from the posterior and data to calculate the proportion of populations of different salmon species and Freshwater Adaptive Zones (FAZs) throughout BC that would be classified as threatened with increasing pressure values.

Simulations

This repo contains code that runs a simple population simulation to explore how changing harvest and productivity through time may affect the observed trend in spawner abundance. This simulation was not described in the paper.

More information

Visit the Salmon Watersheds Program project page and check out the Pacific Salmon Explorer. Questions can be directed at Steph Peacock (speacock at psf dot ca).