Data and code from: Timing matters: Early enrichment reduces vateritic otolith deformities in hatchery-reared coho salmon

Data and code from the manuscript: "Timing matters: Early enrichment reduces vateritic otolith deformities in hatchery-reared coho salmon"This Figshare repository includes all raw data and code used in the manuscript, organized as follows:Enrichment:<b>enrichment.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 in Year 1: control-control, enriched-enriched, and Year 2: control-control, enriched-enriched, control-enriched, and enriched-control.<b>enrichment.pond.release.csv</b><br>A subset of enrichment.csv including only data for fish sampled at first ponding (experiment day 0) and at release (experiment day ~400) for each treatment.<b>EnrichmentAnalysis.Rmd</b> and <b>EnrichmentAnalysis.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.Stocking Density:<b>density.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 in Year 1 and Year 2: low, medium, and high stocking density.<b>density.pond.release.csv</b><br>A subset of density.csv including only data for fish sampled at first ponding (experiment day 0) and at release (experiment day ~400) for each treatment.<b>DensityAnalysis.Rmd</b> and <b>DensityAnalysis.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.<br><br>In all 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.

本数据集配套学术论文"时机至关重要：早期环境富集可降低人工繁育银大麻哈鱼（coho salmon）的球霰石（vaterite）耳石畸形"。本Figshare仓库包含该论文中使用的全部原始数据与代码，整理结构如下：

## 环境富集相关
1. **enrichment.csv**：收录第1年（对照组-对照组、富集组-富集组）及第2年（对照组-对照组、富集组-富集组、对照组-富集组、富集组-对照组）各处理组中，个体银大麻哈鱼左（L）、右（R）矢耳石（sagittal otolith）的文石（aragonite）与球霰石像素占比原始数据。
2. **enrichment.pond.release.csv**：为enrichment.csv的子集，仅包含各处理组在首次入塘（实验第0天）及放流（实验第~400天）时采样的鱼类数据。
3. **EnrichmentAnalysis.Rmd**与**EnrichmentAnalysis.pdf**：包含全部用于分析球霰石占比及耳石对类型比例随时间变化的R代码与输出结果，分析方法采用零inflated beta广义线性混合模型（zero-inflated beta GLMM）及论文中提及的其他方法。

## 放养密度相关
1. **density.csv**：收录第1年及第2年低、中、高放养密度各处理组中，个体银大麻哈鱼左（L）、右（R）矢耳石的文石与球霰石像素占比原始数据。
2. **density.pond.release.csv**：为density.csv的子集，仅包含各处理组在首次入塘（实验第0天）及放流（实验第~400天）时采样的鱼类数据。
3. **DensityAnalysis.Rmd**与**DensityAnalysis.pdf**：包含全部用于分析球霰石占比及耳石对类型比例随时间变化的R代码与输出结果，分析方法采用零inflated beta广义线性混合模型（zero-inflated beta GLMM）及论文中提及的其他方法。

## 通用数据集说明
所有数据集内，"percent.arag.L"与"percent.vat.L"分别指代左耳石的文石像素占比与球霰石像素占比；"percent.arag.R"与"percent.vat.R"分别指代右耳石的文石像素占比与球霰石像素占比。耳石区域的人工分类及像素占比计算，分别通过Adobe Photoshop手动分类与Python脚本完成。