R codes for simulation testing variety of data poor/rare species estimation method < in preparation >
================
Contributors: Kotaro Ono1*
1 Institute of Marine Research, Bergen, Norway.
* Corresponding author: kotaro.ono@hi.no
The purpose of this github repository is create a spatially explicit simulation framework to generate more "realistic" data from the fishery. The model simulates the abundance in space of k number of species with each species having its own population and movement dynamics. Fishery activity is based on ideal free distribution where fishers distribute their effort based on the expected revenue of the fishing grounds. The spatial extent of each fisher can be specify so that some might only fish in certain area of the simulated space. Primary sampling unit is then either a vessel or a haul and we can specify different level of sampling intensity depending on the scenario examined. In this repository, you will find the necessary R- and C++ code to run the simulation, and fit a variey of data poor models.
The code is available in the R/ folder and divided into different scripts. In short, the R/OM.R file specifies the scenario and runs estimation methods. The remaining scripts are utlity functions to run the spatial explicit population dynamics model under the conditions specified in R/OM.R or run the probabilistic sampling for data collection, and more.
Some models (i.e. the multispecies DFA ) are implemented using Template Model Builder (TMB) and the C++ code can be found in the src/ folder.
Documentation about the model will be added into the docs/ folder
Kotaro Ono - kotkot
This project is licensed under the GNU GPLv3 License - see LICENSE for details.
...
