Data and code for manuscript: "Drought-induced sympatry of two salmonid species: Feeding ecology and trophic niches of potential competitors."

Overview This repository contains the input data files, R code, and compiled markdown outputs used to conduct all statistical analyses, construct figures, and generate tables associated with the manuscript titled "Drought-induced sympatry of two salmonid species: Feeding ecology and trophic niches of potential competitors." The repository is organized into two primary subdirectories: Gut_Content_Code_Data/— Contains all code and datasets required to reproduce the gut content analyses (GCA) and associated metrics: Index of Relative Importance (IRI), Schoener's Similarity Index (Schoener's D), Indicator Species Analysis (IndVal), Nonmetric multidimensional scaling (NMDS), and Analysis of Similarities (ANOSIM). Stable_Isotope_Code_Data/ — Contains all code and datasets required to reproduce the stable isotope analyses (SIA), standard ellipse metrics (SIBER), and niche overlap estimates (nicheROVER). File Details and Data Dictionary 1. Gut_Content_Code_Data Lagoon_GCA.Rmd: R Markdown file detailing the step-by-step workflow, calculations, figures, and tables for fish gut content analysis. Lagoon_GCA.html: Self-contained compiled HTML report including all code chunks, console outputs, and generated plots/figures. Lagoon_GCA_Input_Data/: Directory containing seven input datasets for gut content processing and analysis: OUT.Consumed.csv (Full dataset containing raw individual fish diet prey counts and measurements; 332 observations of 26 variables) IRI_input.csv (Formatted input datasets used to calculate monthly Index of Relative Importance values) IRI_input_entirestudy.csv (Formatted input datasets used to calculate overall Index of Relative Importance values) DietR_Sankey_Coho.csv (Coho salmon-specific matrix data formatted for generating diet flow/Sankey network visualizations) DietR_Sankey_Steelhead.csv (Steelhead-specific matrix data formatted for generating diet flow/Sankey network visualizations) DietR_IRI_Output_entirestudy.csv (Summary output file generated during IRI metrics processing) TaxaGroupings.csv (Taxonomic lookup table mapping individual prey taxa to aggregated functional prey categories; Table 1 in main manuscript) 2. Stable_Isotope_Code_Data An important note on software prerequisites and dependencies:To reproduce the stable isotope analyses, the user must install the **JAGS** (Just Another Gibbs Sampler) software. JAGS is an external dependency required for the Bayesian modeling in the `SIBER` package. Because JAGS is an external system-level software, R cannot install it automatically for the user as part of the script. JAGS can be downloaded from [JAGS SourceForge](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/). The scripts were verified using JAGS v 4.3.1 (macOS) and v4.3.2 (Windows). Lagoon_SIA.Rmd: R Markdown file detailing the workflow for lipid correction, summary metrics, non-parametric tests, SIBER ellipse modeling, and nicheROVER overlap probability modeling. Lagoon_SIA.html: Compiled HTML report displaying code executions, diagnostic plots, and tabular outputs. Lagoon_SIA_Input_Data/: Directory containing input data for stable isotope processing: Lagoon_fish_isotope.csv (Stable isotope dataset for age-1+ coho salmon and steelhead, includes additional fish metadata)