Dataset DOI: 10.5061/dryad.rr4xgxdpm

Description of the data and file structure

These data were collected as part of a global study investigating associations between shark hosts and companion species across three ocean basins. Observations were compiled from standardized marine video surveys and associated environmental datasets to examine patterns in companion abundance and distribution relative to shark species, environmental conditions, and spatial variables. The study combined biological observations with environmental and spatial predictor variables, including sea surface temperature, salinity, dissolved oxygen, primary productivity, depth, wind conditions, distance to shore, and distance to port. Additional variables describing marine protection and vulnerability classifications were included to assess potential ecological and management influences on companion associations.

Files and variables

File: No_Outliers.csv

Description: Curated dataset used for all final statistical analyses and modelling presented in the manuscript. The dataset contains cleaned observational records after removal of identified outliers and incomplete records used during model fitting and validation procedures.

Variables

• Op_Code – Unique observation or deployment identifier
• Host_Name – Common name of shark host species
• Family – Taxonomic family of host species
• Species – Scientific name of shark host species
• Loc – Sampling location
• Region – Geographic region
• Ocean – Ocean basin
• SizeClass – Host size classification category
• Fl(cm) – Fork length of host individual (cm)
• Comp_Abund – Companion abundance count
• Species – Shark host species identity
• windU – Wind U-component
• windV – Wind V-component
• SST – Sea surface temperature
• logDepth – Log-transformed depth
• logSalinity – Log-transformed salinity
• logPP – Log-transformed primary productivity
• logPPsquared – Squared log-transformed primary productivity term
• logDFS – Log-transformed distance from shore
• logDTP – Log-transformed distance to port
• Oxy – Dissolved oxygen
• logCHl – Log-transformed chlorophyll concentration
• DVHP – High protection category classification
• DVPP – Vulnerability/protection category classification

Note: the column host fork length contains N/A values in cases where measurements could not be taken. this column is not used in the final analysis.

File: manuscript_main_analysis_datafiles.xlsx

Description: Complete compiled dataset containing all collected observational data associated with the study, including both records retained and excluded from final analyses. This file serves as the master dataset archive for the project.

Variables

• Op_Code – Unique deployment or observation identifier for each BRUVS sample
• Protected – Protection status of the sampling location (e.g., protected or unprotected area)
• Host – Scientific name of the shark host species
• Host_Name – Unique identifier assigned to each host shark individual
• NumCompanions – Total number of companion individuals associated with the host
• ComDiversity – Number of companion species associated with the host (species richness)
• LengthH(mm) – Estimated length of the host shark (mm)
• Host_Surface_Area – calculated body surface area of the host shark (m²)
• Companion – Scientific name of the companion species
• Companion_Name – Unique identifier assigned to each companion individual
• Num – Number of individuals represented by the observation record
• lengthC(mm) – Estimated length of the companion individual (mm)
• DistanceFromHost(mm) – Distance between the companion and host individual (mm)
• Appendage – Host body region or appendage nearest to the companion (e.g., head, dorsal fin, pectoral fin, trunk, caudal fin)
• ActivityC – Behavioural activity category recorded for the companion individual
• dist_port_KM – Distance from the sampling location to the nearest port (km)
• chlorophyll – Surface chlorophyll-a concentration (mg m⁻³)
• primary-production – Primary productivity at the sampling location (mg C m⁻² day⁻¹)
• oxygen – Dissolved oxygen concentration (mmol m⁻³)
• Dist_from_shore_KM – Distance from the sampling location to the nearest shoreline (km)
• Depth_M – Seafloor depth at the sampling location (m)
• Salinity – Sea surface salinity (Practical Salinity Units, PSU)
• SST – Sea surface temperature (°C)

Note: N/A values in cases where measurements could not be taken.

File: companion_associations_2026.R

Description: Main R analysis script used to conduct statistical analyses and generate outputs for the manuscript. The script performs data loading, preprocessing, hurdle negative binomial modelling, model selection, cross-validation, calibration analyses, ROC/AUC diagnostics, and figure generation. The script was developed for use with R version 4.3 or later and requires the R packages listed within the script header.

Code/software

All datasets are provided in Microsoft Excel (.xlsx) format and can be viewed using Microsoft Excel, LibreOffice Calc, Google Sheets, or other spreadsheet software capable of reading .xlsx files.

All analyses were conducted in R version 4.3 or later using the script:

• companion_associations_2026.R

The analytical workflow included:

1. Data import and preprocessing
2. Data cleaning and outlier removal
3. Hurdle negative binomial model fitting
4. Model selection using AICc and BIC
5. Cross-validation and calibration analyses
6. ROC/AUC diagnostic analyses
7. Generation of partial effect plots and manuscript figures

The primary input dataset for analyses was:

• No_Outliers.xlsx

Required R packages include:

• readxl
• dplyr
• tidyr
• tibble
• purrr
• glmmTMB
• AICcmodavg
• glue
• furrr
• future
• R.utils
• pscl
• readr
• caret
• pROC
• ggplot2
• patchwork
• scales

Outputs generated by the script include model rankings, cross-validation statistics, calibration plots, ROC analyses, and partial effect figures saved to the designated output directory.

Access information

Other publicly accessible locations of the data:

• GitHub repository containing datasets, analysis scripts, and project documentation:
  https://github.com/JettWalker/companion_associations_2025

Data was derived from the following sources:

• Data on companions and hosts were compiled from standardized marine ecological observation datasets from BRUVS (Baited Remote Underwater Video Systems). all data was collected by the Marine Futures Lab at the University of Western Australia (https://www.meeuwig.org/)
• Environmental predictor variables were derived from publicly available global oceanographic and spatial datasets from Copernicus Marine (https://marine.copernicus.eu/access-data/), as well as geospatial marine datasets from GEBCO (General Bathymetric Chart of the Oceans) (https://www.gebco.net/) and Global Fishing Watch (https://globalfishingwatch.org/)

License information:

All original data and code associated with this repository are provided for research and educational purposes. Users should cite the associated manuscript and repository when reusing these materials. Third-party environmental datasets remain subject to their original licensing and attribution requirements.