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columbia_sar

A repo to estimate columbia steelhead SARs and explore explanatory variables

creelanalysis

A repository to estimate catch and effort based on "roving-roving" (roving CPUE and roving effort) survey designs

creelestimates_publication

WDFW freshwater creel estimates

cwt_sar_analysis

Automated retrieval, data manipulation, and smolt to adult survival estimation based on coded wire tag data from RMIS

example-models

Example models for Stan

fish_distribution_functions

a repo to house misc fish distribution scripts for WA

genetic_runtiming_samplesize

Simulations to determine how many subsamples of a tissue collection to genotype to accurately identify run type (spring, summer, fall or winter/summer) composition in salmon

hatchery_inseason_forecast

In-season forecasts of hatchery returns

hooking_mortality

A project to estimate hooking mortality for salmon and steelhead using recreational fishing gear

kalama-winter-steelhead-expansions-below-kfh

Kalama Winter Steelhead Expansions Below KFH using Natural Origin Spawner estimates abvove the falls to predict Total Spawner Abundance below the falls with Multivariate Autoregressive State Space models

lcr_coho_escapement

A model to estimate coho salmon spawner escapement for Washington State populations in the Lower Columbia ESU

lcr_steelhead_phos

a with code to estimate pHOS for lower Columbia River steelhead

salmon_forecast_example

salmon_inseason_forecasts

SARIMA Models to estimates in-season run size for salmon and steelhead

salmon_seeding

skagit-river-steelhead-forecast

Reproducible analysis for generating annual abundance forecasts for Skagit River Steelhead

spi_cleanup

cleanup and retrieval of spi data from dwg

st-ipm

Spatiotemporal Integrated Population Model for Coho Salmon Population Dynamcis Modelling

streamflow_tools

a repository with functions to make streamflow downloads easier from USGS and WA DOE, and to interpolate missing or bad gauge data using MARSS models

wdfw_sos_analysis

Project of R and Stan code to complete WDFW analysis for 2020 State Of the Salmon Report

wind_steelhead_jumper_estimates

A repository of code to estimate wild summer steelhead abundance in the Wind River, WA using the mark recapture, census counts at a fish ladder during a period when no steelhead jump the falls, and census counts at the ladder expanded by the ratio of jumping to non-jumping steelhead during the period that jumping occurs.