Reproducibility package for: An autonomous imaging system for reef fish monitoring in the southern Gulf of Mexico

Abstract

This reproducibility package accompanies the manuscript “An autonomous imaging system for reef fish monitoring in the southern Gulf of Mexico”, submitted to Frontiers in Marine Science. Version 2.0.0 corresponds to the revised analytical workflow developed during peer review. The package contains the data, analytical inputs, R code, supplementary tables, reference figures, and documentation required to reproduce the final analyses and publication outputs presented in the revised manuscript, including Figures 2–8 and Supplementary Figures S1–S2 and Tables S1–S3. The package includes a documented, branch-based reproducibility workflow; machine-readable data and analytical matrices; portable R scripts; software-environment and data-dictionary documentation; a file manifest and SHA-256 checksums; and final reference outputs for validation. Figure 5 was generated in R, including the final nMDS ordinations and graphical production. The nested ANOSIM analyses reported with Figure 5 were performed in PRIMER v8. The author-created PRIMER workspace and corresponding open-format inputs and results are included to preserve reproducibility of that statistical component; PRIMER software is not distributed. Computer-vision-derived ecological analyses use frozen inference outputs from the RF-DETR Medium model archived separately in the canonical RF-DETR v1.0.1 reproducibility release (DOI: 10.5281/zenodo.23005643). Reproduction of the ecological analyses does not require model retraining or re-inference. Image preprocessing and sampling provenance is linked to cam2model v0.3.0 (tag v0.3.0; commit ba757e7d4fbbb48582d1168c48d1a48c3bcf3e9a). Historical random sampling does not need to be rerun to reproduce the published analyses. The complete reproducibility package is distributed as SAMP_reproducibility_v2.0.0.zip. See the included README.md, RUN_ORDER.md, DATA_DICTIONARY.md, MANIFEST.csv, and CHECKSUMS.sha256 for package structure, execution order, data definitions, provenance, and integrity verification.