Confident intervals

{ggplot} package

library(ggplot2)
data.estimates = data.frame(
  var   = c('1', '2', '3', '4', '5', '6', '7', '8', '9'),
  par = c(1.12210,0.18489,1.22011,1.027446235,0.43521,0.53464,1.93316,-0.43806,-0.12029),
  se = c(0.42569,0.32162,0.58351,0.771608551,0.24803,0.65372,0.92717,0.45939,0.51558))

data.estimates$idr <- exp(data.estimates$par)

data.estimates$upper <- exp(data.estimates$par + (1.96*data.estimates$se))

data.estimates$lower <- exp(data.estimates$par - (1.96*data.estimates$se))

p2 <- ggplot(data.estimates, aes(var,idr, size=10)) + theme_bw(base_size=10)
p2 + geom_point() + geom_errorbar(aes(x = var, ymin = lower, ymax = upper, size=2), width = 0.2) +  
     scale_y_log10(limits=c(0.1, 50), breaks=c(0.1, 0.5, 1, 5, 10, 25, 50)) + xlab("Site") + ylab("RR")

{plotrix} package

#install.packages("plotrix")
require(plotrix)

## Loading required package: plotrix

par(mfrow=c(1,2))

#Dataset 1

upperlimit = c(10,12,8,14)
lowerlimit = c(5,9,4,7)
mean = c(8,10,6,12)

df = data.frame(cbind(upperlimit,lowerlimit,mean))

plot(df$mean, ylim = c(0,30), xlim = c(1,4))


plotCI(df$mean,y=NULL, uiw=df$upperlimit-df$mean, liw=df$mean-df$lowerlimit, err="y",      
       pch=20, slty=3, scol = "black", add=TRUE)

#Dataset 2

upperlimit_2 = upperlimit*1.5
lowerlimit_2 = lowerlimit*0.8
mean_2 = upperlimit_2-lowerlimit_2

df_2 = data.frame(cbind(upperlimit_2,lowerlimit_2,mean_2))

plot(df$mean_2, ylim = c(0,30), xlim = c(1,4))

plotCI(df_2$mean_2,y=NULL, uiw=df_2$upperlimit_2-df_2$mean_2, liw=df_2$mean_2-   df_2$lowerlimit_2, err="y", pch=20, slty=3, scol = "black", add=TRUE)

rm(upperlimit,lowerlimit,mean,df,upperlimit_2,lowerlimit_2,mean_2,df_2) #remove the objects stored from workspace

par(mfrow=c(1,1)) # go back to default (one graph at a time)