Nothing
## ----pressure, echo=FALSE, fig.align="left", fig.cap="**Figure 1.** Illustration of movements between nodes. Each time step depicts movements during one time unit, for example, a day. The network has *N=4* nodes where node *1* is infected and nodes *2*--*4* are non-infected. Arrows indicate movements of individuals from a source node to a destination node and labels denote the size of the shipment. Here, infection may spread from node *1* to node *3* at *t=2* and then from node *3* to node *2* at *t=3*.", out.width = '100%'----
knitr::include_graphics("img/temporal-network.svg")
## ----eval = TRUE, echo = TRUE, message = FALSE----------------------
events <- data.frame(
event = rep("extTrans", 6), ## Event "extTrans" is
## a movement between nodes
time = c(1, 1, 2, 2, 3, 3), ## The time that the event happens
node = c(3, 3, 1, 4, 3, 4), ## In which node does the event occur
dest = c(4, 2, 3, 3, 2, 2), ## Which node is the destination node
n = c(9, 2, 8, 3, 5, 4), ## How many individuals are moved
proportion = c(0, 0, 0, 0, 0, 0), ## This is not used when n > 0
select = c(4, 4, 4, 4, 4, 4), ## Use the 4th column in
## the model select matrix
shift = c(0, 0, 0, 0, 0, 0)) ## Not used in this example
## -------------------------------------------------------------------
events
## -------------------------------------------------------------------
library(SimInf)
model <- SIR(u0 = data.frame(S = c(10, 15, 20, 25),
I = c(5, 0, 0, 0),
R = c(0, 0, 0, 0)),
tspan = 0:3,
beta = 0,
gamma = 0,
events = events)
## -------------------------------------------------------------------
model@events@E
## -------------------------------------------------------------------
set.seed(1)
set_num_threads(1)
result <- run(model)
## ----fig.width=7, fig.height=4, fig.align="left", fig.cap="**Figure 2.** Number of susceptible, infected and recovered individuals in each node."----
plot(result, range = FALSE)
## -------------------------------------------------------------------
trajectory(result)
## -------------------------------------------------------------------
u0 <- data.frame(S = c(100, 0),
I = c(100, 0),
R = c(100, 0))
## -------------------------------------------------------------------
events <- data.frame(
event = rep("extTrans", 300), ## Event "extTrans" is a movement between nodes
time = 1:300, ## The time that the event happens
node = 1, ## In which node does the event occur
dest = 2, ## Which node is the destination node
n = 1, ## How many individuals are moved
proportion = 0, ## This is not used when n > 0
select = 4, ## Use the 4th column in the model select matrix
shift = 0) ## Not used in this example
## -------------------------------------------------------------------
model <- SIR(u0 = u0,
tspan = 1:300,
events = events,
beta = 0,
gamma = 0)
## ----fig.width=7, fig.height=4, fig.align="left", fig.cap="**Figure 3.** The individuals have an equal probability of being selected regardless of compartment."----
plot(run(model), index = 2)
## ----fig.width=7, fig.height=4, fig.align="left", fig.cap="**Figure 4.** The individuals in the $I$ compartment are more likely of being selected for a movement event."----
model@events@E[2, 4] <- 2
plot(run(model), index = 2)
## ----fig.width=7, fig.height=4, fig.align="left", fig.cap="**Figure 5.** The individuals in the $I$ compartment are even more likely of being selected for a movement event compared to the previous example."----
model@events@E[2, 4] <- 10
plot(run(model), index = 2)
## ----fig.width=7, fig.height=4, fig.align="left", fig.cap="**Figure 6.** The individuals in the $I$ and $R$ compartments are more likely of being selected for a movement event compared to individuals in the $S$ compartment."----
model@events@E[3, 4] <- 4
plot(run(model), index = 2)
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