Data and code from: Hatchery-reared coho salmon develop less otolith deformities in tanks with alternating water flow directions

Data and code from the manuscript: "Hatchery-reared coho salmon develop less otolith deformities in tanks with alternating water flow directions"This Figshare repository includes all raw data and code used in the manuscript, organized as follows:Otolith Examination:<b>flow.csv</b><br>Contains raw data on the percent coverage of aragonite and vaterite for the left (L) and right (R) sagittal otoliths of individual coho salmon from each treatment (alternating, clockwise, counterclockwise) and tank across two experimental years.<b>flow.pond.release.csv</b><br>A subset of flow.csv including only data for fish sampled at first ponding (experiment day 0) and at release (experiment day ~400) for each treatment.In both datasets:"percent.arag.L" and "percent.vat.L" refer to the percentage of aragonite and vaterite pixels in the left otolith, respectively."percent.arag.R" and "percent.vat.R" refer to the percentage of aragonite and vaterite pixels in the right otolith, respectively.Measurements were generated by manually classifying otolith regions in Adobe Photoshop and calculating pixel coverage using a Python script.Representative otolith images and details of the classification workflow are provided in the main manuscript figures and Methods section. The full image dataset is available from the corresponding author upon reasonable request, but is not required to reproduce the analyses.<b>FlowTrialsStats.Rmd</b> and <b>FlowTrialsStats.pdf</b><br>Contain all R code and output used to analyze vaterite coverage and otolith pair type proportions over time using zero-inflated beta GLMMs and other methods described in the manuscript.Survival Analyses:<b>bottleneck_locations_2024-01-09.xlsx</b><br>Provides latitude and longitude coordinates for the PIT-tag antenna arrays installed in the Goldstream River.<b>goldstream_detections_2024-11-15.csv</b><br>Contains PIT-tag detection records for juvenile and returning adult coho salmon, including timestamps, PIT tag IDs, and detection array IDs.<b>Goldstream coho_Detection_Efficiency.R</b><br>R code for calculating PIT antenna detection efficiencies following the method of Connolly (2010), incorporating Wilson’s 95% confidence intervals.<b>Goldstream coho_SAR analyses.R</b><br>R code for estimating survival to adult return (SAR) rates adjusted for detection efficiencies and for conducting logistic regression analyses on individual PIT-tag survival outcomes.<br>