ss3sim: An R Package for Fisheries Stock Assessment Simulation with Stock Synthesis

ss3sim: An R Package for Fisheries Stock Assessment Simulation with Stock Synthesis

Simulation testing is an important approach to evaluating fishery stock assessment methods. In the last decade, the fisheries stock assessment modeling framework Stock Synthesis (SS3) has become widely used around the world. However, there lacks a generalized and scriptable framework for SS3 simulation testing. Here, we introduce ss3sim, an R package that facilitates reproducible, flexible, and...

Tagging Methods for Stock Assessment and Research in Fisheries

International Fisheries Agreements with a Shifting Stock

When a fish stock shifts from one nation to another nation, e.g. due to climate change, the nation that loses the resource has incentives to deplete it while the other nation, receiving the resource, has incentives to conserve it. We propose an analytical model to study under which circumstances self-enforcing agreements can align incentives. Our setup allows to distinguish between a fast and a...

Expectation-Stock Dynamics in Multi-Agent Fisheries

In this paper we consider a game-theoretic dynamic model describing the exploitation of a renewable resource. Our model is based on a Cournot oligopoly game where n profit-maximizing players harvest fish and sell their catch on m markets. We assume that the players do not know the law governing the reproduction of the resource. Instead they use an adaptive updating scheme to forecast the future...

phylodyn: an R package for phylodynamic simulation

10 We introduce phylodyn, an R package for phylodynamic analysis based on gene 11 genealogies. The package main functionality is Bayesian nonparametric estimation of 12 effective population size fluctuations over time. Our implementation includes sev13 eral Markov chain Monte Carlo-based methods and an integrated nested Laplace 14 approximation-based approach for phylodynamic inference that hav...