SacRivSSN

Code and data products associated with the manuscript:

A Dendritic Strontium River Isoscape for Fisheries Applications in the Sacramento River Basin, California, USA

Kyle G. Brennan¹*, Anna M. Sturrock²˒³, Malte Willmes⁴, Kohma Arai³, Corey C. Phillis⁵, Peter K. Weber⁶, and Rachel C. Johnson³˒⁷

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Affiliations

¹ University of Utah, Department of Geology and Geophysics, Salt Lake City, UT, USA
² School of Life Sciences, University of Essex, Colchester, UK
³ Center for Watershed Science, University of California, Davis, CA, USA
⁴ Norwegian Institute for Nature Research, Trondheim, Norway
⁵ The Metropolitan Water District of Southern California, Sacramento, CA, USA
⁶ Lawrence Livermore National Laboratory, Livermore, CA, USA
⁷ Fisheries Ecology Division, Southwest Fisheries Science Center, NMFS, Santa Cruz, CA, USA

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*Corresponding author: kyle.brennan@utah.edu

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Repository structure

out/

R scripts used to reproduce the analyses and figures in the manuscript.

• FD_sacriv_SSNM.R
  Builds the Sacramento River Basin spatial stream network model (SSNM) for river-water 87Sr/86Sr.

• FD_sacriv_wildkings.R
  Generates probabilistic natal-origin and early-rearing habitat maps for example wild adult Chinook salmon using the Sacramento River 87Sr/86Sr isoscape.

• SacRiv_otolith_assignment_workflow.R
  Interactive workflow for assigning otolith 87Sr/86Sr transect intervals to the Sacramento River Basin dendritic isoscape.

• FD_sacriv_fig2_3_4.R
  Reproduces the workflows for manuscript Figures 2, 3, and 4, including 87Sr/86Sr diversity histograms and uncertainty-informed isotopic suite maps.

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data/

Input data used by the scripts in this repository.

Data archived on Zenodo

Most full data products supporting the manuscript are archived at:
DOI: https://doi.org/10.5281/zenodo.17595030

These include:

• sacriv32224.ssn.zip
  Sacramento River spatial stream network object.

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Data included directly in this GitHub repository

• intersected_lines.RDS
  Sacramento River 87Sr/86Sr isoscape stream-line object for present-day assignments.

• otolith_ref_data_sac_hatcheries(all).csv
  Hatchery reference otolith dataset used to estimate within-population / within-site error for Bayesian probabilistic assignments.

• sac_sites_clean.RDS
  Cleaned river-water sampling sites used for SSNM development. Duplicate site observations were summarized, yielding 106 sites used in FD_sacriv_SSNM.R.

• wr_sub.csv
  Subset of endangered winter-run Chinook salmon otolith transects used in manuscript Figure 6 taken from Phillis et al. (2018).

• WR_allSr_forR.csv
  Full endangered winter-run Chinook otolith transects dataset from Phillis et al. (2018).

• srbiso_full.RDS
  Full Sacramento River Basin strontium river isoscape, including above-dam river environments.

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How to use this repository

A typical workflow is:

1. Run FD_sacriv_SSNM.R
   to build or inspect the Sacramento River 87Sr/86Sr spatial stream network model.

2. Run FD_sacriv_fig2_3_4.R
   to reproduce manuscript Figures 2, 3, and 4.

3. Run SacRiv_otolith_assignment_workflow.R
   to interactively inspect otolith transects and generate natal and rearing assignment maps.

4. Run FD_sacriv_wildkings.R
   for the manuscript example fish assignment analyses.

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Required R packages

The scripts in this repository use the following R packages: sf dplyr readr ggplot2 tmap plotly patchwork RColorBrewer purrr tibble tidyr

Notes

• All scripts use relative paths assuming the repository structure shown above.
• Larger data products are archived on Zenodo and not stored directly in GitHub.
• The out/ directory contains analysis scripts (not just output figures).

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Citation

If you use this repository or associated data products, please cite the manuscript and Zenodo archive:

• Manuscript: A Dendritic Strontium River Isoscape for Fisheries Applications in the Sacramento River Basin, California, USA
• Publisher: North American Journal of Fisheries Management (2026)
• Data archive: https://doi.org/10.5281/zenodo.17595030 scales