Body growth, somatic condition and gonad development of Norwegian spring spawning herring (Clupea harengus) linked to large-scale spatiotemporal dynamics in distribution
Contributors: Eydna Í Homrum1*, Guðmundur J. Óskarsson2, Kotaro Ono3, Sondre Hølleland3, Aril Slotte3
1 Faroe Marine Research Institute, Tórshavn, Faroe Islands,
2 Marine and Freshwater Institute, Hafnafjörður, Iceland
3 Institute of Marine Research, Bergen, Norway.
* Corresponding author: eydnap@hav.fo
Link to published paper goes here
The purpose of this github repository is to ensure transparency of the results presented in Homrum et. al. (2022). Here you will find the necessary R- and C++ code to fit the models and produce most of the figures in the paper. Due to restrictions detailed below, the data is not included, but may be shared upon request.
The code is available in the R/ folder and divided into different scripts. Each script will save the results in the output folder and this is then loaded (if needed) in the other scripts. Each script start with a clean R environment. No result files are uploaded to github, but should be reproducible by executing the code in the folders (following the numbering). In short, the R/0_data.R file organizes the data, R/1_analysis.R fits all the models and stores them in the output folder. The remaining scripts creates plots based on the data and the fitted models. The script R/residual_diagnostics.R contains helping functions for residual analysis.
The models are implemented using Template Model Builder (TMB) and the C++ code can be found in the src/ folder.
The data used by Homrum et. al. (2022) were compiled from national databases and stored offline. They can only be accessed by the consent of all parties. Requests to access these datasets should be directed to Guðmundur J. Óskarsson (gjos@hafogvatn.is), Aril Slotte (aril.slotte@hi.no) and Jan Arge Jacobsen (janarge@hav.fo).
Kotaro Ono - kotkot
Sondre Hølleland - holleland
Eydna Í Homrum - eydnaihomrum
This project is licensed under the GNU GPLv3 License - see LICENSE for details.
This study was partly funded by the project “Sustainable multi-species harvest from the Norwegian Sea and adjacent ecosystems” the Research Council of Norway (project number 299554).
Homrum, E.Í., Óskarsson, G.J., Ono, K., Hølleland, S., and Slotte, A. (2022). Body growth, somatic condition and gonad development of Norwegian spring spawning herring (Clupea harengus) linked to large-scale spatiotemporal dynamics in distribution. Manuscript under review in Frontiers of Marine Science.
