This repository contains the source code for the model estimating marine survival of Atlantic salmon using time series abundance data of returning adults and outmigrating smolts, written both in Stan and TMB (although the Stan version is the most up-to-date and the one used for publication).
The Stan model used in for publication defined in analysis/survival_hier_ncp_annualcvs.stan.
The TMB model is defined in
analysis/lc_model_hierarchical.cpp but was not actively developed; it is left
here as a reference.
The non-hierarchical version of the model (i.e. where survival is estimates for
individual populations) is defined in analysis/lc_model.cpp.
So far, the rivers for we have sufficient data to run the model for are:
- LaHave River, NS
- Nashwaak River, NB (St John River)
- Conne River, NL
- Campbellton River, NL
- Western Arm Brook, NL
- Saint-Jean River, QC
- Trinité River, QC
These data are loaded from separate repositories but merged into .rds files for easier use.
The model is hierarchical in the estimation of Pr, where the yearly value of this parameter is estimated based on a population-level distribution, which has relatively informative priors for each river based on their known life histories, and also in the estimation of true smolt abundance, which is done ona population-level basis.