Alternating ecosystem states driven by an invasive fish in a life-history intraguild predation system: Model code and input data

Model code and input data for the multi-state age-structured walleye population model presented by Walsworth et al. in "Alternating ecosystem states driven by an invasive fish in a life-history intraguild predation system", accepted at Canadian Journal of Fisheries and Aquatic Sciences (2025). The model in the manuscript can be run from the R file "Walsworth_etal_WalleyeModel_Code_and_Figures.r", which will read in data from "Walsworth_etal_WalleyeModel_InputData.rdata" and call the JAGS model from file "Walsworth_etal_WalleyeModel.bug". The code will fit the model and produce figures found in manuscript. Figures 5 and 6 require additional simulations, with code provided prior to the figure code. Model code for alternative parameterizations 1, 2, and 4 described in the supplemental material can be found in files "Walsworth_etal_WalleyeModel_Alt1_RWsd1.bug", "Walsworth_etal_WalleyeModel_Alt2_RWsdGamma.bug", and "Walsworth_etal_WalleyeModel_Alt4_LNDaphSmeltObs.bug". Alternative model 3 uses the baseline model ("Walsworth_etal_WalleyeModel.bug"), but uses Daphnia observations from June only, and requires the data set "Walsworth_etal_WalleyeModel_InputData_JuneD.rdata". Alternative model 4 requires the input data found in "Walsworth_etal_WalleyeModel_InputData_lognormal.rdata". Code to run the alternative parameterizations can be found in the R file "Walsworth_etal_WalleyeModel_Code_and_Figures_AlternativeParameterizations_Share.r". Raw data used in the analyses can be found in the .xlsx file "Walsworth_etal_HorsetoothReservoirWalleye_RawData.xlsx", with tabs for the data and column descriptions.