library(igraph)
# random graph
g = sample_gnm(100, 200)
# SIR model simulation
# beta: Non-negative scalar. The rate of infection of an individual
# that is susceptible and has a single infected neighbor
# gamma: Positive scalar. The rate of recovery of an infected individual
sm = sir(g, beta=5, gamma=1, no.sim = 100)
# plot infected
plot(sm, comp = "NI")
# plot susceptibles
plot(sm, comp = "NS")
# plot removed
plot(sm, comp = "NR")
# median and quantile of S, I and R
median(sm)
## $NS
## [0,0.268] (0.268,0.537] (0.537,0.805] (0.805,1.07] (1.07,1.34]
## 82.0 41.0 10.0 3.0 2.0
## (1.34,1.61] (1.61,1.88] (1.88,2.15] (2.15,2.41] (2.41,2.68]
## 2.0 2.0 2.0 2.0 2.0
## (2.68,2.95] (2.95,3.22] (3.22,3.49] (3.49,3.76] (3.76,4.02]
## 2.0 2.0 2.0 2.0 2.0
## (4.02,4.29] (4.29,4.56] (4.56,4.83] (4.83,5.1] (5.1,5.37]
## 1.0 2.0 2.0 1.0 2.0
## (5.37,5.63] (5.63,5.9] (5.9,6.17] (6.17,6.44] (6.44,6.71]
## 2.0 1.0 1.5 1.0 1.5
## (6.71,6.98] (6.98,7.24] (7.24,7.51] (7.51,7.78] (7.78,8.05]
## 2.0 2.5 NA NA 1.5
## (8.05,8.32] (8.32,8.59] (8.59,8.85] (8.85,9.12] (9.12,9.39]
## NA NA NA 1.0 0.0
##
## $NI
## [0,0.268] (0.268,0.537] (0.537,0.805] (0.805,1.07] (1.07,1.34]
## 17.0 52.0 66.0 57.0 44.0
## (1.34,1.61] (1.61,1.88] (1.88,2.15] (2.15,2.41] (2.41,2.68]
## 34.0 26.0 20.0 15.0 11.0
## (2.68,2.95] (2.95,3.22] (3.22,3.49] (3.49,3.76] (3.76,4.02]
## 8.0 6.0 5.0 4.0 3.0
## (4.02,4.29] (4.29,4.56] (4.56,4.83] (4.83,5.1] (5.1,5.37]
## 2.0 2.0 1.0 1.0 1.0
## (5.37,5.63] (5.63,5.9] (5.9,6.17] (6.17,6.44] (6.44,6.71]
## 0.0 0.0 0.0 0.0 0.0
## (6.71,6.98] (6.98,7.24] (7.24,7.51] (7.51,7.78] (7.78,8.05]
## 0.0 0.0 NA NA 0.5
## (8.05,8.32] (8.32,8.59] (8.59,8.85] (8.85,9.12] (9.12,9.39]
## NA NA NA 0.0 0.0
##
## $NR
## [0,0.268] (0.268,0.537] (0.537,0.805] (0.805,1.07] (1.07,1.34]
## 1.0 6.0 20.0 39.0 54.0
## (1.34,1.61] (1.61,1.88] (1.88,2.15] (2.15,2.41] (2.41,2.68]
## 64.0 72.0 79.0 83.0 87.0
## (2.68,2.95] (2.95,3.22] (3.22,3.49] (3.49,3.76] (3.76,4.02]
## 90.0 92.0 93.0 94.0 95.0
## (4.02,4.29] (4.29,4.56] (4.56,4.83] (4.83,5.1] (5.1,5.37]
## 96.0 96.0 97.0 97.0 97.0
## (5.37,5.63] (5.63,5.9] (5.9,6.17] (6.17,6.44] (6.44,6.71]
## 98.0 98.0 98.5 99.0 98.5
## (6.71,6.98] (6.98,7.24] (7.24,7.51] (7.51,7.78] (7.78,8.05]
## 98.0 97.5 NA NA 98.0
## (8.05,8.32] (8.32,8.59] (8.59,8.85] (8.85,9.12] (9.12,9.39]
## NA NA NA 99.0 100.0
quantile(sm, comp = "NI", prob = 0.50)
## [0,0.268] (0.268,0.537] (0.537,0.805] (0.805,1.07] (1.07,1.34]
## 17.0 52.0 66.0 57.0 44.0
## (1.34,1.61] (1.61,1.88] (1.88,2.15] (2.15,2.41] (2.41,2.68]
## 34.0 26.0 20.0 15.0 11.0
## (2.68,2.95] (2.95,3.22] (3.22,3.49] (3.49,3.76] (3.76,4.02]
## 8.0 6.0 5.0 4.0 3.0
## (4.02,4.29] (4.29,4.56] (4.56,4.83] (4.83,5.1] (5.1,5.37]
## 2.0 2.0 1.0 1.0 1.0
## (5.37,5.63] (5.63,5.9] (5.9,6.17] (6.17,6.44] (6.44,6.71]
## 0.0 0.0 0.0 0.0 0.0
## (6.71,6.98] (6.98,7.24] (7.24,7.51] (7.51,7.78] (7.78,8.05]
## 0.0 0.0 NA NA 0.5
## (8.05,8.32] (8.32,8.59] (8.59,8.85] (8.85,9.12] (9.12,9.39]
## NA NA NA 0.0 0.0