Sacramento River winter-run Chinook salmon cohort reconstruction – data and code

Maturation schedules shape a population’s age structure and influence productivity and exposure to fishing. Fish cultivated and raised in artificial environments like hatcheries may mature at different ages compared to their natural-origin counterparts. We evaluated whether endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) produced in a conservation hatchery had different maturation schedules compared to natural-origin fish, and how differences affected their exposure to, and impact from, the ocean salmon fishery. Using coded-wire tags collected from hatchery fish in the ocean and in-river fisheries and on the spawning grounds, and scales collected from natural-origin spawner carcasses, we reconstructed the life history of hatchery and natural-origin cohorts from 2002–2015 brood years. Hatchery fish had similar age-2 maturation rates but higher age-3 maturation rates compared to natural-origin fish, resulting in fewer age-4 individuals and an overall more ..., , , # Readme

**Scripts**
1\. CWT Spawning Data Prep\.R – Preparing coded\-wire tag recovery data from spawning grounds and hatchery for hatchery\-origin cohort reconstruction
2\. CWT Harvest Data Prep\.R – Preparing coded\-wire tag recovery data from ocean and in\-river harvest\. Calculating the age\-aggregated encounter rate\.
3\. Hatchery Cohort Reconstruction\.R – Cohort reconstruction code for hatchery cohorts from CWT data\. Calculates hatchery\-origin maturation and impact rates\.
4\. Impact rates shared\.R – Calculating impact rates based on encounter rate and average harvestability and release mortality\.
5\. Hatchery Cohort Reconstruction by sex\.R – Sex\-specific cohort reconstruction code for hatchery cohorts using impact rates from hatchery cohort reconstruction\.
6\. Natural Cohort Reconstruction Prep\.R – Age specific escapement based on scale data\.  Kimura Chikuni adjustments
7\. Natural Cohort Reconstruction\.R \- Cohort reconstruction code for natural cohorts\. Calculates...