Table 1.

Description of the user functions associated with the toolbox.

Function	Role
options_fit.m	Specifies the parameters related to model fitting, including the time series data characteristics, the model, parameter estimation method, error structure, and calibration period. The structure of the options_fit.m file is given in Supplementary Text S1 (supplementary file 1).
options_forecast.m	Specifies the parameters related to model forecasting, including the forecasting period, the calibration period, the characteristics of the time series data, the model, parameter estimation method, and the error structure. The structure of the options_forecast.m file is given in Supplementary Text S2 (supplementary file 1).
plotODEModel.m	Plots model solutions based on the ODE model, parameter ranges and initial conditions provided by the user in the options_fit.m file.
Run_Fit_ODEModel.m	Fits the ODE model specified by the user to data with quantified uncertainty.
Run_Forecasting_ODEModel.m	Fits the ODE model specified by the user to data with quantified uncertainty and generates a model-based forecast with quantified uncertainty.
plotFit_ODEModel.m	Display the ODE model fit and the empirical distribution of the parameters. It also saves output .csv files in the output folder with the model fit, the parameter estimates, Monte Carlo standard errors, 95% CIs, and the calibration performance metrics.
plotForecast_ODEModel.m	Display the model-based forecast and the performance metrics of the forecast. Moreover, the data associated with the forecasts, the parameter estimates, and the calibration and forecasting performance metrics are saved as .csv files in the output folder.