@article {Moore029777, author = {Christopher M. Moore and Christopher R. Stieha and Ben C. Nolting and Maria K. Cameron and Karen C. Abbott}, title = {QPot: An R Package for Stochastic Differential Equation Quasi-Potential Analysis}, elocation-id = {029777}, year = {2015}, doi = {10.1101/029777}, publisher = {Cold Spring Harbor Laboratory}, abstract = {QPot (pronounced ) is an R package for analyzing two-dimensional systems of stochastic differential equations. It provides users with a wide range of tools to simulate, analyze, and visualize the dynamics of these systems. One of QPot{\textquoteright}s key features is the computation of the quasi-potential, an important tool for studying stochastic systems. Quasi-potentials are particularly useful for comparing the relative stabilities of equilibria in systems with alternative stable states. This paper describes QPot{\textquoteright}s primary functions, and explains how quasi-potentials can yield insights about the dynamics of stochastic systems. Three worked examples guide users through the application of QPot{\textquoteright}s functions.}, URL = {https://www.biorxiv.org/content/early/2015/10/23/029777}, eprint = {https://www.biorxiv.org/content/early/2015/10/23/029777.full.pdf}, journal = {bioRxiv} }