Using lower river genetic stock identification (GSI) and a tributary specific mark-recapture program to estimate genetic unit escapements of Pacific Salmon within large river systems

The data and scripts contained within this repository allow for the reproduction of the analyses described in the manuscript \"Using lower river genetic stock identification (GSI) and a tributary-specific mark-recapture program to estimate genetic unit escapements of Pacific Salmon within large river systems\", an escapement estimation approach that combines lower river genetic stock identification (GSI) with an accurate mark-recapture escapement estimate for a single major spawning tributary (the “reference unit”), with the example under investigation being the Skeena River coho salmon, the Skeena River Tyee test fishery, and the Witset Mark-Recapture program on the Bulkley River. This repository is organized into two pieces. First, a folder containing the genetic data used underlying the methods (Baseline, mixtures, and Colony assignments as made). Second, a folder containing the R scripts used in executing the analyses. 
, , # Data from: Using lower river genetic stock identification (GSI) and a tributary specific mark-recapture program to estimate genetic unit escapements of Pacific Salmon within large river systems

Dataset DOI: [10.5061/dryad.pzgmsbd2w](https://doi.org/10.5061/dryad.pzgmsbd2w)

## Description of the data and file structure

Data and scripts to perform the analysis in: \"Using lower river genetic stock identification (GSI) and a tributary-specific mark-recapture program to estimate genetic unit escapements of Pacific Salmon within large river systems\".

### Files and variables

#### File: 01_Data_v1.1.zip

**Description:** 

PBT_Colony_Results

* PID20190105_and_more_Skeena_test_GN(19)_and_more_sc240-265-266-306-361-389-434_results.txt.gz - Contains PBT assignments made over the full length of the project, from 2019-2024. Brood-years considered for assignment were 2:-4 from Tyee sampling (e.g., 2024 had brood years 2022-2020 considered.

Skeena_formatted_baseline

* bco_SNP_Skeena_v5.0.1_2..., ,