基于R igraph库的信息传播（Information Diffusion）过程可视化

过程：生成网络；随机选择种子节点，按概率传播；更新图中传播节点信息；按时间线绘图保存。

R代码：

transmission_rate = 0.4
coins = c(1, 0) 
probabilities = c(transmission_rate, 1-transmission_rate )         
# sample(coins, 1, rep=TRUE, prob=probabilities) # Generate a sequence
# toss the coins
toss = function(freq) {
  tossing = NULL
  for (i in 1:freq ) tossing[i] = sample(coins, 1, rep=TRUE, prob=probabilities)
  tossing = sum(tossing)
  return (tossing)
}

#更新感染/传播后的节点
update_diffusers = function(diffusers){
  nearest_neighbors = data.frame(table(unlist(neighborhood(g, 1, diffusers))))
  nearest_neighbors = subset(nearest_neighbors, !(nearest_neighbors[,1]%in%diffusers))
  keep = unlist(lapply(nearest_neighbors[,2], toss))
  new_infected = as.double(as.character(nearest_neighbors[,1][keep >= 1]))
  #the original code in references should be modified to this.
  diffusers = unique(c(diffusers, V(g)[new_infected])) 
  return(diffusers)
  }

node_number = 100
library(igraph)


g = graph.tree(node_number, children = 2)
g = graph.star(node_number)
g = graph.full(node_number)
g = graph.ring(node_number)
g = connect.neighborhood(graph.ring(node_number), 2)


g = erdos.renyi.game(node_number, 0.1)
g = rewire(graph.ring(node_number), with = each_edge(prob = 0.8))
g = watts.strogatz.game(1,node_number,3,0.2) 


# take this network as example
g = barabasi.game(node_number) 
graph_name = "Scale-free network"
plot(g)

seed_num = 1
set.seed(20140301); diffusers = sample(V(g),seed_num)
infected =list()
infected[[1]]= diffusers
# set the color
E(g)$color = "grey"
V(g)$color = "white"


set.seed(2014); layout.old = layout.fruchterman.reingold(g, niter = 1000)
V(g)$color[V(g)%in%diffusers] = "red"
plot(g, layout =layout.old)


total_time = 1
while(length(infected[[total_time]]) < node_number){ 
  infected[[total_time+1]] = sort(update_diffusers(infected[[total_time]]))
  cat(length(infected[[total_time + 1]]), "-->")
  total_time = total_time + 1
}


plot_time_series = function(infected, m){
  num_cum = unlist(lapply(1:m, 
            function(x) length(infected[[x]]) ))
  p_cum = num_cum/node_number
  p = diff(c(0, p_cum))
  time = 1:m
  plot(p_cum~time, type = "b", 
       ylab = "CDF", xlab = "Time",
       xlim = c(0,total_time), ylim =c(0,1))
  plot(p~time, type = "h", frame.plot = FALSE,
       ylab = "PDF", xlab = "Time",
       xlim = c(0,total_time), ylim =c(0,1))
}

plot_time_series(infected, 16)

plot_gif = function(infected){
  m = 1
  while(m <= length(infected)){
    layout(matrix(c(1, 2, 1, 3), 2,2, byrow = TRUE), widths=c(3,1), heights=c(1, 1))
    V(g)$color = "white"
    V(g)$color[V(g)%in%infected[[m]]] = "red"
    plot(g, layout =layout.old, edge.arrow.size=0.2)
    title(paste(graph_name, "\n Transmission Rate =", transmission_rate, ", Day", m))
    plot_time_series(infected, m)
    m = m + 1}
}

library(animation)
plot_gif(infected)

saveGIF({
  ani.options("convert")
  plot_gif(infected)
}, ani.width = 800, ani.height = 500)

参考：
https://chengjunwang.com/network-diffusion 代码需要修改才能正常运行，本文代码主要来源于此。
https://github.com/chengjun/networkdiffusion 代码需要修改才能正常运行，包装成R package形式更方便使用。