#d0 is the distribution on the right, with the greater mean
#dz is the distribution on the left, with the lower mean


#d0=density(z$calf.ratio[6,1,,])
#dz=density(z$calf.ratio[6,2,,])
#
#
#lower=calf.ci[1]
#upper=calf.ci[2]
#type="between"

#manage_plot(z.0=z$phi[6,1,,], z.treat=z$phi[6,5,,], lower=.08, type="below",label= "Probability of infection", panel="A", xlim=c(0,.8))

manage_plot=function(z.0, z.treat,upper=NA, lower=NA, type, label,panel, xlim){

d0=density(z.0)
dz=density(z.treat)

x0=as.vector(d0$x)
y0=as.vector(d0$y)
xz=as.vector(dz$x)
yz=as.vector(dz$y)



plot(x0,y0,xlab=label, main=panel,typ="l",ylim=c(0,1.3*max(dz$y)), lwd=2, ylab="Density", col="grey")
lines(xz,yz, lwd=2, col="black")
		
if(type == "between"){
m = cbind(x0,y0)
m=m[m[,1] > lower,] 
M=m[m[,1]< upper,]


xx=c(M[,1],rev(M[,1]))
yy=c(M[,2],rep(0,length(M[,2])))

#the .99 is to prevent polygon from blocking the line for the pdf
polygon(xx,yy,col=topo.colors(5,alpha=.3), border=NA)

m = cbind(xz,yz)
m=m[m[,1] > lower,] 
M2=m[m[,1]< upper,]
xx=c(M2[,1],rev(M2[,1]))
yy=c(M2[,2],rep(0,length(M2[,2])))
polygon(xx,yy,density=10,border=NA)

abline(h=0)
abline(v=lower, lty="dashed")
abline(v=upper,lty="dashed")


}

if(type == "below"){
m = cbind(xz,yz)
M=m[m[,1]< lower,]
xx=c(M[,1],rev(M[,1]))
yy=c(M[,2],rep(0,length(M[,2])))

polygon(xx,yy,density=10,border=NA)
m = cbind(x0,y0)
 M2=m[m[,1]< lower,]
xx=c(M2[,1],rev(M2[,1]))
yy=c(M2[,2],rep(0,length(M2[,2])))
polygon(xx,yy,col=topo.colors(5,alpha=.3))
lines(xz,yz, lwd=2, col="black")

abline(v=lower, lty="dashed")
abline(h=0)
}

if(type == "above"){
m = cbind(x0,y0)
M=m[m[,1] > upper,]
xx=c(M[,1],rev(M[,1]))
yy=c(M[,2],rep(0,length(M[,2])))
polygon(xx,yy,col=topo.colors(5,alpha=.3))
 m = cbind(xz,yz)
 M2=m[m[,1] > upper,]
xx=c(M2[,1],rev(M2[,1]))
yy=c(M2[,2],rep(0,length(M2[,2])))
polygon(xx,yy,density=10,border=NA)

lines(xz,yz, lwd=2, col="black")

abline(v=upper, lty="dashed")
abline(h=0)
}

} #end of function