Display the outcome from a simulated trajectory

Plot either the median and the quantile range of the counts in all nodes, or plot the counts in specified nodes.

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,
  ...
)

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.

...

Other graphical parameters that are passed on to the plot function.

Examples

if (FALSE) { # \dontrun{
## For reproducibility, call the set.seed() function and specify
## the number of threads to use. To use all available threads,
## remove the set_num_threads() call.
set.seed(123)
set_num_threads(1)

## Create an 'SIR' model with 100 nodes and initialise
## it with 990 susceptible individuals and 10 infected
## individuals in each node. Run the model over 100 days.
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 and save the result.
result <- run(model)

## Plot the median and interquartile range of the number
## of susceptible, infected and recovered individuals.
plot(result)

## Plot the median and the middle 95\
## number of susceptible, infected and recovered individuals.
plot(result, range = 0.95)

## Plot the median and interquartile range of the  number
## of infected individuals.
plot(result, "I")

## Use the formula notation instead to plot the median and
## interquartile range of the number of infected individuals.
plot(result, ~I)

## Plot the number of susceptible, infected
## and recovered individuals in the first
## three nodes.
plot(result, index = 1:3, range = FALSE)

## Use plot type line instead.
plot(result, index = 1:3, range = FALSE, type = "l")

## Plot the number of infected individuals in the first node.
plot(result, "I", index = 1, range = FALSE)

## Plot the proportion of infected individuals (cases)
## in the population.
plot(result, I ~ S + I + R)

## Plot the proportion of nodes with infected individuals.
plot(result, I ~ S + I + R, level = 2)

## Plot the median and interquartile range of the proportion
## of infected individuals in each node
plot(result, I ~ S + I + R, level = 3)

## Plot the proportion of infected individuals in the first
## three nodes.
plot(result, I ~ S + I + R, level = 3, index = 1:3, range = FALSE)
} # }