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library(igraph)
setwd("Documents/Cascade Project/Raw Data/")
load('chi-19mar2015.RData')
d = remove.edge.attribute(person,'weight')
lcc = induced.subgraph(d,which(clusters(d)$membership==which.max(clusters(d)$csize)))
##### Small-World Analysis
trl = mean(transitivity(lcc,type='local',isolates='zero'))
apl = average.path.length(lcc)
cat('Local Transitivity =', trl);cat('\nAverage Path Length =', apl)
nsim = 5
ER_sim = data.frame(trl=rep(0,nsim),apl=0)
for(i in 1:nsim){
print(i)
erg = erdos.renyi.game(n=vcount(lcc),p.or.m=ecount(lcc),type='gnm')
erg = induced.subgraph(erg,which(clusters(erg)$membership==which.max(clusters(erg)$csize)))
ER_sim[i,1] = mean(transitivity(erg,type='local',isolates='zero'))
ER_sim[i,2] = average.path.length(erg)
}
S = data.frame(C_dat = trl,
L_dat = apl,
C_ER=mean(ER_sim$trl),
L_ER=mean(ER_sim$apl),
S_ER=mean((trl/ER_sim$trl)/(apl/ER_sim$apl)))
S
##### Degree Distribution
plot(degree.distribution(lcc)*vcount(lcc),log='xy',type='l',col='red',lwd=2,
xlab='Degree', ylab='Number of Vertices', main='Degree Distribution')
##### Victims
vic_ids = which(V(lcc)$vic==TRUE)
non_vic_ids = which(V(lcc)$vic==FALSE)
hist(as.numeric(V(lcc)$vic_date[vic_ids]),100,col='lightblue',
xlab='Day of Study Period',main='Infections During the Study Period')
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