https://github.com/cran/meta
Tip revision: 131c044d999a05b848d6c1b20918cfd7dec89467 authored by Guido Schwarzer on 09 October 2009, 00:00:00 UTC
version 1.1-2
version 1.1-2
Tip revision: 131c044
metainf.R
metainf <- function(x, pooled, sortvar, level=x$level, level.comb=x$level.comb){
if (!inherits(x, "meta"))
stop("Argument 'x' must be an object of class \"meta\"")
if (missing(pooled)){
if (length(x$comb.fixed)==0 & length(x$comb.random)==0)
pooled <- "fixed"
if (length(x$comb.fixed)>0 & length(x$comb.random)==0)
if (x$comb.fixed) pooled <- "fixed"
else pooled <- "NoNe"
if (length(x$comb.fixed)==0 & length(x$comb.random)>0)
if (x$comb.random) pooled <- "random"
else pooled <- "NoNe"
if (length(x$comb.fixed)>0 & length(x$comb.random)>0){
if (x$comb.fixed)
pooled <- "fixed"
if (!x$comb.fixed & x$comb.random)
pooled <- "random"
if (!x$comb.fixed & !x$comb.random)
pooled <- "NoNe"
}
}
##
if (pooled=="NoNe")
stop("Parameters \"comb.fixed\" and \"comb.random\" in object '",
deparse(substitute(x)),
"' are either 'FALSE' or 'NULL'. ",
"Please use argument \"pooled=fixed\" or \"pooled=random\" ",
"to select meta-analytical model.")
imeth <- charmatch(tolower(pooled), c("fixed", "random"), nomatch = NA)
##
if (is.na(imeth))
stop("'pooled' should be \"fixed\" or \"random\"")
##
pooled <- c("fixed", "random")[imeth]
if (length(level)==0){
warning("level set to 0.95")
level <- 0.95
}
##
if (length(level.comb)==0){
warning("level.comb set to 0.95")
level.comb <- 0.95
}
k.all <- length(x$TE)
sort <- !missing(sortvar)
sm <- x$sm
if (!sort) sortvar <- rep(1, k.all)
if (sort & length(sortvar) != k.all)
stop("'x' and 'sortvar' have different length")
n.e <- x$n.e
n.c <- x$n.c
n <- x$n
##
event.e <- x$event.e
event.c <- x$event.c
event <- x$event
##
mean.e <- x$mean.e
mean.c <- x$mean.c
##
sd.e <- x$sd.e
sd.c <- x$sd.c
##
TE <- x$TE
seTE <- x$seTE
##
studlab <- x$studlab
sortvar <- sortvar
if (sort){
##
o <- order(sortvar)
##
n.e <- n.e[o]
n.c <- n.c[o]
n <- n[o]
##
event.e <- event.e[o]
event.c <- event.c[o]
event <- event[o]
##
mean.e <- mean.e[o]
mean.c <- mean.c[o]
##
sd.e <- sd.e[o]
sd.c <- sd.c[o]
##
TE <- TE[o]
seTE <- seTE[o]
##
studlab <- studlab[o]
sortvar <- sortvar[o]
}
res.i <- matrix(NA, ncol=6, nrow=k.all)
##
for (i in 1:k.all){
sel <- -i
##
if (inherits(x, "metabin")){
##
## To get rid of warning message
## "For a single trial, inverse variance method used
## instead of Mantel Haenszel method."
##
oldopt <- options(warn=-1)
m <- metabin(event.e[sel], n.e[sel], event.c[sel], n.c[sel],
method=x$method, sm=sm,
incr=x$incr, allincr=x$allincr, addincr=x$addincr,
allstudies=x$allstudies, MH.exact=x$MH.exact,
RR.cochrane=x$RR.cochrane,
level=level, level.comb=level.comb,
warn=x$warn)
options(oldopt)
}
##
if (inherits(x, "metacont")){
m <- metacont(n.e[sel], mean.e[sel], sd.e[sel],
n.c[sel], mean.c[sel], sd.c[sel], sm=sm,
level=level, level.comb=level.comb)
}
##
if (inherits(x, "metagen")){
m <- metagen(TE[sel], seTE[sel], sm=sm,
level=level, level.comb=level.comb)
}
##
if (inherits(x, "metaprop")){
m <- metaprop(event[sel], n[sel],
studlab=studlab[sel],
freeman.tukey=x$freeman.tukey,
level=level, level.comb=level.comb)
sm <- "AS prop"
}
##
tsum.i <- summary(m)
##
if (pooled == "fixed"){
res.i[i,] <- c(m$TE.fixed, m$seTE.fixed,
tsum.i$fixed$p, tsum.i$I2$TE,
tsum.i$tau, sum(m$w.fixed, na.rm=TRUE))
}
##
else if (pooled == "random"){
res.i[i,] <- c(m$TE.random, m$seTE.random,
tsum.i$random$p, tsum.i$I2$TE,
tsum.i$tau, sum(m$w.random, na.rm=TRUE))
}
}
tsum <- summary(x, level=level, level.comb=level.comb)
##
if (pooled == "fixed"){
TE.sum <- x$TE.fixed
seTE.sum <- x$seTE.fixed
pval.sum <- tsum$fixed$p
w.sum <- sum(x$w.fixed, na.rm=TRUE)
}
##
else if (pooled == "random"){
TE.sum <- x$TE.random
seTE.sum <- x$seTE.random
pval.sum <- tsum$random$p
w.sum <- sum(x$w.random, na.rm=TRUE)
}
slab <- c(paste("Omitting", studlab), "Pooled estimate")
res <- list(TE=c(res.i[,1], NA, TE.sum),
seTE=c(res.i[,2], NA, seTE.sum),
studlab=c(rev(rev(slab)[-1]), " ", rev(slab)[1]),
p.value=c(res.i[,3], NA, pval.sum),
w=c(res.i[,6], NA, w.sum),
I2=c(res.i[,4], NA, tsum$I2$TE),
tau=c(res.i[,5], NA, tsum$tau),
sm=sm, method=x$method, k=x$k,
pooled=pooled,
TE.fixed=NA, seTE.fixed=NA,
TE.random=NA, seTE.random=NA,
Q=NA, tau=NA,
level=level, level.comb=level.comb)
class(res) <- c("metainf", "meta")
res
}