Multisp_model_JAE

Model and data used in the following paper:

Trijoulet V., Fay G. and Miller T.J. 2019 Performance of a state-space multispecies model: what are the consequences of ignoring predation and process errors in stock assessments? Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.13515

Scripts:

• The estimation models (EMs) can be fitted from the "Fitting_the_EMs.R" file
• The structural code is in the file "MS_SSM.cpp"
• Functions used in the cpp code are in "MS_SSM_functions.h"
• The script "MS_SSM_make.map.fn.R" is the function that creates the map argument of the objective function depending on the options chosen in the models
• The script "MS_SSM_make.random.fn.R" is the function that creates the random argument of the objective function depending on the options chosen in the models

Data:

• The 1000 data sets used in the paper are available as lists in "sim_data_all.RData" (downloadable at https://doi.org/10.5281/zenodo.3407512)
• A set of initial values is available in "init.RData"

Please note:

This model is not the most recent version of the multispecies model and it appears as it was used in the paper. A new and improved version of the model is available in the repository "MS_SSM". Please consider this latter repository for an updated version of the model.