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 characteristics of the time series data, the model, the parameter estimation method, the error structure, and the calibration period. The structure of the options_fit.m file is described in Text 1S (supplementary file 1) |
options_forecast.m | Specifies the parameters related to model forecasting, including the characteristics of the time series data, the model, the parameter estimation method, the error structure, the calibration period, and forecasting period. The structure of the options_forecast.m file is described in Text 2S (supplementary file 1) |
options_Rt.m | Specifies the parameters related to the estimation of the effective reproduction number, namely the type of generation interval distribution and the mean and variance of the generation interval for the infectious disease of interest |
plotGrowthModel.m | Plots model solutions where the user provides the type of growth model, parameter values, and the initial condition |
Run_Fit_GrowthModels.m | Fits a model to data with quantified uncertainty |
Run_Forecasting_GrowthModels.m | Fits a model to data with quantified uncertainty and generates a model-based forecast with quantified uncertainty |
plotFit_GrowthModels | Displays the model fit and the empirical distribution of the estimated parameters. It also saves output .csv files in the output folder with the model fit, the parameter estimates with 95% confidence intervals (CIs), the calibration performance metrics, and the doubling times estimated from the incidence trajectory |
plotForecast_GrowthModels | Displays the model-based forecast and the associated performance metrics. Moreover, the data associated with the forecasts, the parameter estimates, the doubling times estimated from the incidence trajectory, and the calibration and forecasting performance metrics, are saved as .csv files in the output folder |
plotFit_ReproductionNumber | Displays the model fit and the effective reproduction number. It also saves .csv files in the output folder with the model fit, the parameter estimates with 95% CIs, the calibration performance metrics, and the doubling times estimated from the incidence trajectory |
plotForecast_ReproductionNumber | Displays the model-based forecast and the corresponding effective reproduction number. Moreover, the data associated with the forecasts, the parameter estimates, the doubling times estimated from the incidence trajectory, and the calibration and forecasting performance metrics, are saved as .csv files in the output folder |
