R/sumlog.R

In metap: Meta-Analysis of Significance Values

sumlog <-
function(p, log.p = FALSE) {
   keep <- (p > 0) & (p <= 1)
   invalid <- sum(1L * keep) < 2
   if(invalid) {
      warning("Must have at least two valid p values")
      res <- list(chisq = NA_real_, df = NA_integer_,
         p = NA_real_, validp = p[keep])
   } else {
      lnp <- log(p[keep])
      chisq <- (-2) * sum(lnp)
      df <- 2 * length(lnp)
      if(length(lnp) != length(p)) {
         warning("Some studies omitted")
      }
      res <- list(chisq = chisq, df = df,
         p = pchisq(chisq, df, lower.tail = FALSE,
            log.p = log.p), validp = p[keep])
    }
   class(res) <- c("sumlog", "metap")
   res
}
print.sumlog <- function(x, ...) {
   cat("chisq = ", x$chisq, " with df = ", x$df, " p = ", x$p, "\n")
   invisible(x)
}