##
## Version 4.9-5 or above of R package meta is needed to use lower and
## upper CI limits directly in R function metagen()
##
## At the moment (13-02-19), this version is only available on GitHub
##
install.packages("devtools")
devtools::install_github("guido-s/meta")


## Make R package meta available and
## - print results with two significant digits
## - use Cochrane layout for forest plots
##
library(meta)
settings.meta(digits = 2, layout = "RevMan5")


## Data from Steurer et al. (2006), Analysis 1.1 Overall survival
## https://www.cochranelibrary.com/cdsr/doi/10.1002/14651858.CD004270.pub2/abstract
##
##
study <- c("FCG on CLL 1996", "Leporrier 2001", "Rai 2000", "Robak 2000")
logHR <- c(-0.592, -0.0791, -0.237, 0.163)
selogHR <- c(0.345, 0.0787, 0.144, 0.312)


## Conduct meta-analysis using log hazard ratios and standard errors
##
m1 <- metagen(logHR, selogHR, studlab = study, sm = "HR")
##
m1
##
forest(m1)
grid::grid.text("Meta-analysis using log hazard ratios and standard errors",
                0.5, 0.94, gp = grid::gpar(cex = 1.5))


## Conduct meta-analysis using HRs and 95%-CIs
##
HR <- c(0.55, 0.92, 0.79, 1.18)
lower.HR <- c(0.28, 0.79, 0.59, 0.64)
upper.HR <- c(1.09, 1.08, 1.05, 2.17)
##
## Input must be log hazard ratios, not hazard ratios
##
m2 <- metagen(log(HR), lower = log(lower.HR), upper = log(upper.HR),
              studlab = study, sm = "HR")
##
m2
##
forest(m2)
grid::grid.text("Meta-analysis using hazard ratios and confidence limits",
                0.5, 0.94, gp = grid::gpar(cex = 1.5))