plot,SimInf_model-method {SimInf} | 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, legend = NULL, col = NULL, lty = NULL, lwd = 2, compartments = NULL, node = NULL, range = 0.5, ...)
x |
The |
legend |
The character vector to appear in the legend. Default is to use the names of the compartments. |
col |
The plotting color for each compartment. Default is black. |
lty |
The line type for each compartment. Default is the sequence: 1=solid, 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash. |
lwd |
The line width for each compartment. Default is 2. |
compartments |
Character vector with the compartments in the
model to include in the plot. Default is |
node |
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 |
... |
Additional arguments affecting the plot produced. |
## Not run: ## 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, compartments = "I") ## Plot the number of susceptible, infected ## and recovered individuals in the first ## three nodes. plot(result, node = 1:3, range = FALSE) ## Plot the number of infected individuals in the first node. plot(result, compartments = "I", node = 1, range = FALSE) ## End(Not run)