From 1739e9f5706bb8a73de5dbf0b467de49ea040898 Mon Sep 17 00:00:00 2001 From: Ben Green Date: Mon, 8 Jun 2015 15:21:51 -0400 Subject: added my R scripts --- R Scripts/data-exploration.R | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100755 R Scripts/data-exploration.R (limited to 'R Scripts/data-exploration.R') diff --git a/R Scripts/data-exploration.R b/R Scripts/data-exploration.R new file mode 100755 index 0000000..404ce9e --- /dev/null +++ b/R Scripts/data-exploration.R @@ -0,0 +1,40 @@ +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') + -- cgit v1.2.3-70-g09d2