Oxygen-deficit history predicts biological recovery debt after dissolved-oxygen compliance in managed freshwaters
Description
This dataset and code repository supports the manuscript “Oxygen-deficit history predicts biological recovery debt after dissolved-oxygen compliance in managed freshwaters”. The study combines high-frequency dissolved-oxygen monitoring, a controlled prior oxygen-history recovery experiment in juvenile bighead carp and grass carp, and independent managed-waterbody low-oxygen–reoxygenation event validation. The repository contains processed data, source tables, model outputs, codebook files and R scripts used to reproduce the oxygen-history descriptors, recovery-debt indices and external validation model comparison reported in the manuscript. The deposited files include field dissolved-oxygen logger summaries, oxygen-deficit duration and cumulative deficit-load metrics, achieved exposure and water-quality tables, respirometry-derived recovery-debt data, systemic physiological records, metabolic and branchial recovery-debt summaries, targeted protein-level stress-response summaries, integrated recovery-debt index outputs, independent external validation stage-level input data and Table 3 model-comparison outputs. The primary external validation model comparison uses 20 event/reference-window × sampling-stage summaries. Fish-level Field RDI records were used to estimate stage-level means and uncertainty, but were not used as independent rows in the primary AICc, CV-RMSE, leave-one-event-out CV-RMSE, marginal R² or calibration-slope model comparison.
Files
Steps to reproduce
1. Download and unzip WR_DO_recovery_Mendeley_DIRECT_UPLOAD_v1.zip. 2. Inspect README.md, CODEBOOK.md and FILE_MANIFEST_SHA256.csv to verify the repository structure, file descriptions and checksums. 3. Use data/processed/external_validation_stage_level_input.csv as the primary input for the external validation model comparison. This file contains 20 event/reference-window × sampling-stage summaries. 4. Run scripts/00_install_packages.R to install or check required R packages. 5. Run scripts/01_validate_input_files.R to check expected input files and column structure. 6. Run scripts/02_validate_submission_tables.R to validate the submitted main and supplementary table files. 7. Run scripts/03_external_validation_stage_level_models.R to reproduce the stage-level external validation model comparison reported in Table 3. 8. Run scripts/99_run_all.R to execute the full validation workflow. 9. The recomputed Table 3 model-comparison output is written to outputs/tables/table3_external_validation_model_comparison_recomputed.csv.
Institutions
- China Three Gorges UniversityHubei, Yichang