plot,SimInf_model-method | R Documentation |
Plot either the median and the quantile range of the counts in all nodes, or plot the counts in specified nodes.
## S4 method for signature 'SimInf_model' plot( x, y, level = 1, index = NULL, range = 0.5, type = "s", lwd = 2, frame.plot = FALSE, legend = TRUE, ... )
x |
The |
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, |
level |
The level at which the prevalence is calculated at
each time point in |
index |
Indices specifying the nodes to include when plotting
data. Plot one line for each node. Default ( |
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 |
type |
The type of plot to draw. The default |
lwd |
The line width. Default is |
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. |
## 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\% quantile range of the ## 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)
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