SimInf (version 11.1.0)

plot,SimInf_model-method: Display the outcome from a simulated trajectory

Description

Plot the median and quantile range of the counts in all nodes, the counts in specified nodes, or the prevalence of a disease. The function supports formula notation for specifying compartments and prevalence calculations.

Usage

# S4 method for SimInf_model
plot(
  x,
  y,
  level = 1,
  index = NULL,
  range = 0.5,
  type = "s",
  lwd = 2,
  frame.plot = FALSE,
  legend = TRUE,
  log = "",
  ...
)

Arguments

x

The model to plot.

y

Character vector or formula with the compartments in the model to include in the plot. Default includes all compartments in the model. Can also be a formula that specifies the compartments that define the cases with a disease or that have a specific characteristic (numerator), and the compartments that define the entire population of interest (denominator). The left-hand-side of the formula defines the cases, and the right-hand-side defines the population, for example, I~S+I+R in a ‘SIR’ model (see ‘Examples’). The . (dot) is expanded to all compartments, for example, I~. is expanded to I~S+I+R in a ‘SIR’ model (see ‘Examples’).

level

The level at which the prevalence is calculated at each time point in tspan. 1 (population prevalence): calculates the proportion of the individuals (cases) in the population. 2 (node prevalence): calculates the proportion of nodes with at least one case. 3 (within-node prevalence): calculates the proportion of cases within each node. Default is 1.

index

Indices specifying the nodes to include when plotting data. Plot one line for each node. Default (index = NULL) is to extract data from all nodes and plot the median count for the specified compartments.

range

Show the quantile range of the count in each compartment. Default is to show the interquartile range i.e. the middle 50% of the count in transparent color. The median value is shown in the same color. Use range = 0.95 to show the middle 95% of the count. To display individual lines for each node, specify range = FALSE.

type

The type of plot to draw. The default type = "s" draws stair steps. See base plot for other values.

lwd

The line width. Default is 2.

frame.plot

a logical indicating whether a box should be drawn around the plot.

legend

a logical indicating whether a legend for the compartments should be added to the plot. A legend is not drawn for a prevalence plot.

log

A character string which contains "x" if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic.

...

Other graphical parameters (e.g. xlab, ylab, main) that are passed on to the plot function.

Details

For a comprehensive tutorial with detailed explanations and more examples, see the vignette("Post-process data in a trajectory", package = "SimInf").

Examples

## For reproducibility, specify the number of threads.
set_num_threads(1)

## Create an 'SIR' model with 100 nodes.
model <- SIR(u0 = data.frame(S = rep(990, 100),
                             I = rep(10, 100),
                             R = rep(0, 100)),
             tspan = 1:100,
             beta = 0.16,
             gamma = 0.077)

## Run the model with a fixed seed for reproducibility.
result <- run(model, seed = 22)

## Plot counts (median and IQR)
plot(result)

## Plot individual trajectories for specific nodes
plot(result, index = 1:3, range = FALSE)

## Plot prevalence (proportion of infected)
plot(result, I ~ S + I + R)

## Customize labels
plot(result, "I", xlab = "Time", ylab = "Count", main = "Infections")