Created
June 1, 2014 04:02
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Simulation of herd immunity
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herd<-function(vaccination.fraction,arrival.rate=1/30,end.of.time=365,frequent.flyers=0.01,annoying.beep=TRUE){ | |
N<-10000 | |
xy<-matrix(runif(2*N),nrow=N,ncol=2) | |
status<-1+rbinom(N,1,vaccination.fraction) | |
startstat<-status | |
par(mar=c(1,1,3,1)) | |
#svir | |
myrisk<-c(.3,.08,1,1,1,1,0) | |
yourrisk<-c(0,0,1,1,1,1,0) | |
nextstat<-c(3,3,4,5,6,7,7) | |
color<-c(adjustcolor(c("black","green","red","red","red","red"),alpha.f=0.5),"royalblue") | |
sym<-c(1,1,rep(19,6)) | |
i<-1 | |
while(i<end.of.time){ | |
if(runif(1)<arrival.rate) { | |
if(annoying.beep) cat("\007") | |
idx<-sample(N,1) | |
status[idx]<-3 | |
startstat[idx]<-NA | |
} | |
dists<-get.knn(xy) | |
prob<- myrisk[status]*rowSums((dists$nn.dist<0.009)*yourrisk[status[dists$nn.index]]) | |
prob[prob>1]<-1 | |
change<-rbinom(N,1,prob) | |
change[myrisk[status]==1]<-1 | |
status[change==1]<-nextstat[status[change==1]] | |
plot(xy,col=color[status],pch=sym[status],axes=FALSE,xlab="",ylab="") | |
xy<-(xy+matrix(rnorm(2*N,s=0.01),nrow=N,ncol=2)) %%1 | |
if (frequent.flyers>0){ | |
idx<-sample(N,N*frequent.flyers) | |
xy[idx,]<-runif(2*length(idx)) | |
} | |
mtext(i,adj=0.5) | |
if (any(status>2 & !is.na(startstat))){ | |
tt<-table(status>2,startstat) | |
mtext(paste("Infected|Not vaccinated =",round(100*tt[2,1]/(tt[2,1]+tt[1,1])),"%",sep=""),adj=0) | |
mtext(paste("Infected|Vaccinated =",round(100*tt[2,2]/(tt[2,2]+tt[1,2])),"%"),adj=1) | |
} | |
i<-i+1 | |
} | |
} | |
# ~/Downloads/ffmpeg -r 3 -i Rplot%d.png -y -vcodec libx264 -pix_fmt yuv420p herd-90.mp4 |
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