Vitense, KelseyHanson, Mark AHerwig, Brian RZimmer, Kyle DFieberg, John R2021-01-202021-01-202021-01-20https://hdl.handle.net/11299/218004Detailed descriptions for each of the files can be found in README.txt. We recommend using RStudio to run the code. Once all files are downloaded to a single directory, double-click on 'HMM.Rproj' to open up a new RStudio window, and the working directory will automatically be set to the folder where the project files are located.This repository contains the data and R code used to conduct the analyses in the article "Using hidden Markov models to inform conservation and management strategies in ecosystems exhibiting alternative stable states" in Journal of Applied Ecology.Attribution-NonCommercial-ShareAlike 3.0 United Statesalternative stable stateshidden Markov modelBayesian statisticslatent variableregime shiftstate space modelshallow lake managementhysteresiseutrophicationDatasethttps://doi.org/10.13020/sm2d-fk79