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# calculate bivariate logits and OR
blogits <- function(Y, add, colnames, row.vars, rev=FALSE) {
if (ncol(Y) != 4) stop("Y must have 4 columns")
if (missing(add)) add <- if (any(Y==0)) 0.5 else 0
Y <- Y + add
if (rev) Y <- Y[,4:1]
L <- matrix(0, nrow(Y), 3)
L[,1] <- log( (Y[,1] + Y[,2]) / (Y[,3] + Y[,4]) )
L[,2] <- log( (Y[,1] + Y[,3]) / (Y[,2] + Y[,4]) )
L[,3] <- log( (Y[,1] * Y[,4]) / ((Y[,2] * Y[,3])) )
cn <- c("logit1", "logit2", "logOR")
colnames(L) <- if(missing(colnames)) cn else c(colnames, cn[-(1:length(colnames))])
if(!missing(row.vars)) L <- cbind(L, row.vars)
L
}
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