Data from: Robust trophic pathways in carnivorous reef fishes across a major human disturbance gradient

This repository contains data and R code associated with the article "Robust trophic pathways in carnivorous reef fishes across a major human disturbance gradient," currently under review.

File Descriptions (data folder)

• ki_bulk_sia_final.csv is a comma-delimited file containing sample meta-data and bulk stable isotope data for sampled carnivorous reef fish.

• ki_csia_c.csv is a comma-delimited file containing sampled meta-data and amino acid-specific stable carbon isotope data for sampled carnivorous reef fish.

• ki_csia_n.csv is a comma-delimited file containing sampled meta-data and amino acid-specific stable nitrogen isotope data for sampled carnivorous reef fish.

• ki_fish_data_sum.csv is a comma-delimited file containing summary data for fish observed in underwater visual census surveys (from Magel et al. 2020).

File Descriptions (analysis folder)

• KI_bulk_SIA.R includes code to characterize variation in reef fish isotopic niche sizes and positions (i.e., Standard Ellipse Areas) via bulk muscle stable carbon (d13C) and nitrogen (d15N) isotope data.

• KI_LDA.R includes code to classify individual carnivorous reef fish to carbon source groups via essential amino acid (EAA) d13C fingerprinting and simple and bootstrapped linear discriminant analysis (LDA).

• KI_trophic_position.R includes code to calculate and compare reef fish trophic positions using amino acid d15N values

• KI_fish_community_metrics.R includes code to create Fig. 1 B-D (multi-panel figure plotting relative biomass and abundance of fish trophic groups at each local human disturbance level)

• summarySE.R is a function to calculate summary statistics

File Descriptions (SIMMs sub-folder)

• KI_SIMM_plots.R includes code to collate and plot SIMM results across species.

• output_diagnostics.R includes code to returns diagnostics for a fit MixSIAR model.

• output_stats.R includes code to return summary statistics from a fit MixSIAR model.

• Species-specific subfolders:

  • KI_mixsiar_XX.R includes code to quantify proportional contributions of carbon sources to individual carnivorous reef fish via essential amino acid (EAA) d13C analysis and Bayesian stable isotope mixing modeling.

  • KI_discrimination.csv is a comma-delimited file containing mean and SDs of discrimination factors used in the SIMMs.

  • KI_sources.csv is a comma-delimited file containing mean and SDs of essential amino acid (EAA) d13C values from the carbon source proxies.

  • KI_fish_CSIA_C_XX.csv is a comma-delimited file containing sample meta-data and amino acid-specific stable carbon isotope data for sampled carnivorous reef fish.

Note: Most figures were further modified using Adobe Illustrator before final publication.