plot-methods: Methods for Function 'plot'

In swash: Health Geography Toolbox for Model-Based Analysis of Infections Panel Data

Methods for Function plot

Description

Methods for function plot for different S4 classes: infpan, sbm, sbm_ci, and loggrowth.

Methods

signature(x = "infpan")

plot.infpan(x, y, ...): Plots regional infections against time

Arguments:

• x: An object of class infpan including infections panel data.

• y: Optional argument for additional customization, such as plot style or axis labels.

• ...: Additional graphical parameters that can be passed to control plot appearance.

Details: This method is used to visualize case data by region for N regions and T time points.

signature(x = "sbm")

plot.sbm(x, y = NULL, col_edges = "blue", xlab_edges = "Time", ylab_edges = "Regions", main_edges = "Edges", col_SIR = c("blue", "red", "green"), lty_SIR = c("solid", "solid", "solid"), lwd_SIR = c(1,1,1), xlab_SIR = "Time", ylab_SIR = "Regions", main_SIR = "SIR integrals", col_cases = "red", lty_cases = "solid", lwd_cases = 1, xlab_cases = "Time", ylab_cases = "Infections", main_cases = "Daily infections", xlab_cum = "Cases", ylab_cum = "Regions", main_cum = "Cumulative infections per region", horiz_cum = TRUE, separate_plots = FALSE):

Plots the results of the Swash-Backwash Model. This generates two plots:

• Edges over time.

• Total infections per time unit.

Arguments:

• x: An object of class sbm representing the results of the Swash-Backwash Model.

• y: Optional argument for additional customization, such as plot style or axis labels.

• ...: Additional graphical parameters that can be passed to control plot appearance.

Details: This method is used to visualize the output of the Swash-Backwash Model, providing insight into the dynamics of the modeled epidemic.

signature(x = "sbm_ci")

plot.sbm_ci(x, y, ...): Plots the results of bootstrap confidence intervals for the Swash-Backwash Model. This generates a single figure with six subplots:

• S_A (susceptible population),

• I_A (infected population),

• R_A (recovered population),

• t_{FE} (final epidemic time),

• t_{LE} (last epidemic time),

• R_{0A} (basic reproduction number).

Arguments:

• x: An object of class sbm_ci containing the bootstrap confidence intervals for the Swash-Backwash Model.

• y: Optional argument for additional customization, such as plot style or axis labels.

• ...: Additional graphical parameters for fine-tuning the plots.

Details: This method is used to visualize the bootstrap confidence intervals for various parameters of the Swash-Backwash Model.

signature(x = "countries")

plot.sbm(x, y = NULL, col_bars = "grey", col_ci = "red"): Plots the results of the between-countries analysis via Swash-Backwash Model. This generates four plots:

• Indicator for country 1

• Indicator for country 2

• Boxplots of the distribution of the indicator in country 1 and 2

• Distribution of the difference between the indicators of country 1 and 2

Arguments:

• x: An object of class countries representing the results of the Swash-Backwash Model country analysis.

• y: Not relevant

• col_bars: Color of bars

• col_ci: Color of confidence intervals

Details: This method is used to visualize the output of the Swash-Backwash Model, providing insight into the dynamics of the modeled epidemic.

signature(x = "loggrowth")

plot.loggrowth(x, y, ...): Plots the results of the logistic growth model, including:

• Observed values

• Predicted values

• First derivative

Arguments:

• x: An object of class loggrowth containing the data for the logistic growth model.

• y: Optional argument for additional customization of the plot (e.g., color, labels).

• ...: Additional arguments for graphical parameters.

Details: This method is useful for visualizing the observed and predicted growth patterns in an epidemic or similar phenomena modeled by logistic growth.

signature(x = "expgrowth")

plot.expgrowth(x, y, ...): Plots the results of the exponentai growth model, including:

• Observed values

• Predicted values

Arguments:

• x: An object of class expgrowth containing the data for the exponential growth model.

• y: Optional argument for additional customization of the plot (e.g., color, labels).

• ...: Additional arguments for graphical parameters.

Details: This method is useful for visualizing the observed and predicted growth patterns in the initial phase of an epidemic or similar phenomena modeled by exponential growth.

signature(x = "hawkes")

plot.hawkes(x, y, ...): Plots the results of the Hawkes process model, including:

• Observed values

• Predicted values

Arguments:

• x: An object of class hawkes containing the data for the Hawkes model.

• y: Optional argument for additional customization of the plot (e.g., color, labels).

• ...: Additional arguments for graphical parameters.

Details: This method is useful for visualizing the observed and predicted growth patterns of an epidemic or similar phenomena modeled as Hawkes processes.

signature(x = "breaksgrowth")

plot.hawkes(x, y, ...): Plots the results of a breakpoint analysis, including:

• Time series data

• Breakpoints

Arguments:

• x: An object of class breaksgrowth containing the data for the breakspoints model.

• y: Optional argument for additional customization of the plot (e.g., color, labels).

• ...: Additional arguments for graphical parameters.

Details: This method is useful for visualizing the derived breakpoints.

Author(s)

Thomas Wieland

swash documentation built on April 7, 2026, 1:06 a.m.