This repo contains R code for analyzing individual-level condition of cod and to contrast the ability, or parsimony, of different variables to explain variation in cod condition, each linked to specific hypothesis proposed in the literature.

We use Spatiotemporal linear mixed-effects models and a predictive-modelling framework within the R package sdmTMB. This repository contains all data and code used for analyses and figures from Lindmark et al (20XX).

Authors: Max Lindmark, Sean Anderson and Michele Casini

data

• Cod, flounder and condition data are downloaded from ICES databases DATRAS
• Oxygen from CTD samples from OCEANOGRAPHY.
• Herring and sprat abundance estimates are from the ICES WGBIFS database for the BIAS survey. Modelled oxygen data stem from the NEMO-Nordic-SCOBI model*, downloaded from EU Copernicus

R Contains code for analysis and data processing

figures Contains figures of results

output Contains .rds objects of model outputs due to long compuation times

References for NEMO-Nordic-SCOBI

Almroth-Rosell, E., Eilola, K., Hordoir, R., Meier, H.E.M., Hall, P.O.J., 2011. Transport of fresh and resuspended particulate organic material in the Baltic Sea — a model study. J.Mar.Sys. 87, 1-12. Doi: 10.1016/j.jmarsys.2011.02.005

Eilola, K., Meier, M.H.E., Almroth, E., 2009. On the dynamics of oxygen, phosphorus and cyanobacteria in the Baltic Sea; A model study. J.Mar.Sys. 75, 163-184. Doi: doi:10.1016/j.jmarsys.2008.08.009.

Kuznetsov, I., Eilola, K., Dieterich, C., Hordoir, R., Axell, L., Höglund, A. and Schimanke, S., 2016. Model study on the variability of ecosystem parameters in the Skagerrak-Kattegat area, effect of load reduction in the North Sea and possible effect of BSAP on Skagerrak-Kattegat area.