Data from: Accounting for movement in spatial surplus production models: A case study of redfish on the Eastern Grand Banks of Newfoundland
Data files
Jul 16, 2025 version files 1.76 MB
-
final_submitted_codes.zip
1.76 MB
-
README.md
2.33 KB
Abstract
Spatial surplus production models (SSPMs) are a key alternative to spatial population dynamics models when reliable spatial aging data is unavailable. However, fish movements present computational challenges for SSPMs and can be confounded with process errors, hindering the identification of SSPM parameters. We propose leveraging a Gaussian Markov Random Field (GMRF) with a Matérn covariance structure to account for spatiotemporal variation in dynamics and population production, thereby circumventing the computational and confounding issues. Through simulation studies, wherein data is generated explicitly considering movements, our novel random field model outperforms the alternative methods in estimating fish spatial abundance, as evaluated using statistical metrics including Akaike information criterion, Bayesian information criteria, and correlation between simulated and estimated populations. We also applied our method to reveal the spatial distribution of redfish in NAFO 3LN divisions based on survey and commercial catch data. Model validation confirms a good fit. Our model's ability to fit relatively short time series data (i.e., eight years) demonstrates the benefits of using the random field approach in data-poor fisheries stock assessments.
Dataset DOI: 10.5061/dryad.rxwdbrvnn
Description of the data and file structure
The final_submitted_codes.zip file contains two folders: simulations and redfish.
1. simulations
This folder includes the TMB codes, R codes and data (i.e., redfish_results.RData) used for the simulation studies presented in the paper:
Accounting for Movement in Spatial Surplus Production Models: A Case Study of Redfish on the Eastern Grand Banks of Newfoundland by Hoang Nguyen, Jin Gao, Noel G. Cadigan, Yanjun Wang, Fan Zhang, Nan Zheng.
The CSV files are containers to store simulation results.
2. redfish
This folder contains the TMB code, R code and data used for the case studies in the paper. The data files include the .RData files and a landings.txt file.
In both folders, the survey data are simulated due to restrictions from the Fisheries and Oceans Canada (DFO) on sharing actual survey data. Nonetheless, the simulated data effectively replicate key characteristics of the real data and are sufficient to demonstrate the performance of the proposed methodology in the paper.
Files and variables
File: final_submitted_codes.zip
Description: This zip file contains two folders: simulations and redfish.
1. simulations
This folder includes the TMB codes, R codes and data (i.e., redfish_results.RData) used for the simulation studies presented in the paper:
Accounting for Movement in Spatial Surplus Production Models: A Case Study of Redfish on the Eastern Grand Banks of Newfoundland by Hoang Nguyen, Jin Gao, Noel G. Cadigan, Yanjun Wang, Fan Zhang, Nan Zheng.
The CSV files are containers to store simulation results.
2. redfish
This folder contains the TMB code, R code and data used for the case studies in the paper. The data files include the .RData files and a landings.txt file.
In both folders, the survey data are simulated due to restrictions from the Fisheries and Oceans Canada (DFO) on sharing actual survey data. Nonetheless, the simulated data effectively replicate key characteristics of the real data and are sufficient to demonstrate the performance of the proposed methodology in the paper.
Code/software
R, any recent versions. TMB package in R.