Display the outcome from a simulated trajectory — plot,SimInf

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 class '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, set the seed and number of threads.
set.seed(123)
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.
result <- run(model)

## 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")