load(file="data/CTADGUM_pred-with-LA.RData") # load(file="data/CTADGUM_pred-no-place-effects.RData")
SCALE <- 10
##TODO## #move to prep file CTADGUM_age1524_2012$LA.Name <- toupper(CTADGUM_age1524_2012$LA.Name) # CTADGUM_age1524_2012$Coverage2012.gum <- CTADGUM_age1524_2012$Chlamydia.Tests.gum*(1-0.0767) #remove proportion estimated to be 15 year olds CTADGUM_age1524_2012$Coverage2012.gum <- with(CTADGUM_age1524_2012, Chlamydia.Tests.gum/X15.24.Year.Old.Population.Estimates) ##TODO## # CTADGUM_age1524_2012$Coverage2012.gum <- with(CTADGUM_age1524_2012, Chlamydia.Tests.gum/X16.24.Year.Old.Population.Estimates) CTADGUM_pred <- merge(CTADGUM_pred, CTADGUM_age1524_2012[ ,c("LA.Name", "Coverage2012.gum")], by.x="LA Name", by.y="LA.Name") CTADGUM_age1524_2013$LA.Name <- toupper(CTADGUM_age1524_2013$LA.Name) # CTADGUM_age1524_2013$Coverage2013.gum <- CTADGUM_age1524_2013$Chlamydia.Tests.gum*(1-0.0767) #remove proportion estimated to be 15 year olds CTADGUM_age1524_2013$Coverage2013.gum <- with(CTADGUM_age1524_2013, Chlamydia.Tests.gum/X15.24.Year.Old.Population.Estimates) ##TODO## # CTADGUM_age1524_2013$Coverage2013.gum <- with(CTADGUM_age1524_2013, Chlamydia.Tests.gum/X16.24.Year.Old.Population.Estimates) CTADGUM_pred <- merge(CTADGUM_pred, CTADGUM_age1524_2013[ ,c("LA.Name", "Coverage2013.gum")], by.x="LA Name", by.y="LA.Name")
plot(CTADGUM_pred$GUMwtmean, CTADGUM_pred$LApred, xlim=c(0,0.3), ylim=c(0,0.3), cex=CTADGUM_pred$NatsalLAsize/SCALE, main="(b)", xlab="Direct LA estimates using Natsal-3", ylab="MRP estimates") abline(a=0, b=1)
par(mfrow=c(1,1)) plot(CTADGUM_pred$LApred, CTADGUM_pred$Coverage2012.gum, cex=CTADGUM_pred$NatsalLAsize/SCALE, xlab="MRP estimates", ylab="Surveillance data", # col=1+as.numeric(CTADGUM_pred$NatsalLAsize!=1.5), xlim=c(0,0.3), ylim=c(0,0.3)) abline(a=0, b=1, lty=2, lwd=2) abline(a=mean.surveil-mean.Natsal, b=1, lty=3, lwd=2) abline(h=mean.Natsal, lty=2) abline(h=mean.surveil, lty=3) text(x = c(0.25, 0.5, 0.25, 0.45), y = c(0.2, 0.3, 0.34, 0.4), labels = c("A","B","C","D"), cex=1.8) par(mfrow=c(1,1)) plot(CTADGUM_pred$LApred, CTADGUM_pred$Coverage2012.gum, xlab="MRP estimates", ylab="Surveillance data", cex=CTADGUM_pred$NatsalLAsize/SCALE, col=rgb(0, 0, 0, 0.3), pch=16, # col=1+as.numeric(CTADGUM_pred$NatsalLAsize!=1.5), xlim=c(0,0.3), ylim=c(0,0.3)) abline(a=0, b=1) par(mfrow=c(1,1)) plot(CTADGUM_pred$LApred, CTADGUM_pred$Coverage2012.gum, xlab="MRP estimates", ylab="Surveillance data", col=rgb(0, 0, 0, 0.3), pch=16, # col=1+as.numeric(CTADGUM_pred$NatsalLAsize!=1.5), xlim=c(0,0.3), ylim=c(0,0.3)) abline(a=0, b=1, lty=2, lwd=2) abline(a=mean.surveil-mean.Natsal, b=1, lty=3, lwd=2) abline(h=mean.Natsal, lty=2) abline(h=mean.surveil, lty=3) text(x = c(0.25, 0.5, 0.25, 0.45), y = c(0.2, 0.3, 0.34, 0.4), labels = c("A","B","C","D"))
par(mfrow=c(1,1)) plot(CTADGUM_pred$LApred, CTADGUM_pred$Coverage2013.gum, cex=CTADGUM_pred$NatsalLAsize/SCALE, xlab="MRP estimates", ylab="Surveillance data", # col=1+as.numeric(CTADGUM_pred$NatsalLAsize!=1.5), xlim=c(0,0.3), ylim=c(0,0.3)) abline(a=0, b=1, lty=2, lwd=2) abline(a=mean.surveil-mean.Natsal, b=1, lty=3, lwd=2) abline(h=mean.Natsal, lty=2) abline(h=mean.surveil, lty=3) text(x = c(0.25, 0.5, 0.25, 0.45), y = c(0.2, 0.3, 0.34, 0.4), labels = c("A","B","C","D"), cex=1.8) par(mfrow=c(1,1)) plot(CTADGUM_pred$LApred, CTADGUM_pred$Coverage2013.gum, xlab="MRP estimates", ylab="Surveillance data", cex=CTADGUM_pred$NatsalLAsize/SCALE, col=rgb(0, 0, 0, 0.3), pch=16, # col=1+as.numeric(CTADGUM_pred$NatsalLAsize!=1.5), xlim=c(0,0.3), ylim=c(0,0.3)) abline(a=0, b=1) par(mfrow=c(1,1)) plot(CTADGUM_pred$LApred, CTADGUM_pred$Coverage2013.gum, xlab="MRP estimates", ylab="Surveillance data", col=rgb(0, 0, 0, 0.3), pch=16, # col=1+as.numeric(CTADGUM_pred$NatsalLAsize!=1.5), xlim=c(0,0.3), ylim=c(0,0.3)) abline(a=0, b=1, lty=2, lwd=2) abline(a=mean.surveil-mean.Natsal, b=1, lty=3, lwd=2) abline(h=mean.Natsal, lty=2) abline(h=mean.surveil, lty=3) text(x = c(0.25, 0.5, 0.25, 0.45), y = c(0.2, 0.3, 0.34, 0.4), labels = c("A","B","C","D"))
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