BUGS code to estimate parameters of a full life cycle model
Outputs of an individual-based model for larval drift and survival that provided yearly estimates of the dispersion and mortality of eggs and larvae, from spawning grounds to settlement in several coastal nurseries;
A habitat suitability model, based on juvenile trawl surveys coupled with a geographic information system, to estimate juvenile densities and surface areas of suitable juvenile habitat in each nursery sector;
A statistical catch-at-age model for the estimation of the numbers-at-age and the fishing mortality on subadults and adults.
The following BUGS code refers to a specific scenario of the larvae to juvenile mortality process tested in the associated paper (see paper). This scenario (R3) assumes a density-independent mortality parameter common to all nurseries (a_BH) and a nursery-specific density-dependent mortality parameter (b_BH).
If you download the following presentation, you will find a presentation of different functions in the R-software useful for spatial data manipulations. Choosing the right libraries allows to create, import, modify, manipulate and map vector (shapefiles) or matrix (raster) spatial data. Your spatial files can then be used for modeling and spatial interpolation like kriging.
The presentation is can be downloaded here, however, this presentation is in French, although images and r-code provided is normally clear enough for anybody to understand.
This presentation has been realized in 2012. There may be some modifications in functions presented. For instance, in library “sp”, fonction overlay() in now called over().
Construction of the Community matrix from Ecopath models
Appendix D. The R (www. r-project.org) code for the sensitivity analysis. The code is given for data stored in a three-sheet Excel file. The original matrix Q is stored in the “net_impacts” sheet and is obtained following steps (i) to (iv) described in Appendix C. The original matrix Q minus 20% is in the “Com_Min” sheet and the original matrix Q plus 20% in the “Com_Max” sheet. They all three give the net impact of a compartment in rows on the compartment in column.