R/rstudent.rma.peto.r

Defines functions rstudent.rma.peto

Documented in rstudent.rma.peto

rstudent.rma.peto <- function(model, digits, progbar=FALSE, ...) {

   mstyle <- .get.mstyle()

   .chkclass(class(model), must="rma.peto")

   na.act <- getOption("na.action")

   if (!is.element(na.act, c("na.omit", "na.exclude", "na.fail", "na.pass")))
      stop(mstyle$stop("Unknown 'na.action' specified under options()."))

   x <- model

   if (missing(digits)) {
      digits <- .get.digits(xdigits=x$digits, dmiss=TRUE)
   } else {
      digits <- .get.digits(digits=digits, xdigits=x$digits, dmiss=FALSE)
   }

   ddd <- list(...)

   .chkdots(ddd, c("time"))

   if (.isTRUE(ddd$time))
      time.start <- proc.time()

   #########################################################################

   delpred  <- rep(NA_real_, x$k.f)
   vdelpred <- rep(NA_real_, x$k.f)

   ### elements that need to be returned

   outlist <- "beta=beta, vb=vb"

   ### note: skipping NA tables

   if (progbar)
      pbar <- pbapply::startpb(min=0, max=x$k.f)

   for (i in seq_len(x$k.f)) {

      if (progbar)
         pbapply::setpb(pbar, i)

      if (!x$not.na[i])
         next

      args <- list(ai=x$outdat.f$ai, bi=x$outdat.f$bi, ci=x$outdat.f$ci, di=x$outdat.f$di, add=x$add, to=x$to, drop00=x$drop00, level=x$level, subset=-i, outlist=outlist)
      res <- try(suppressWarnings(.do.call(rma.peto, args)), silent=TRUE)

      if (inherits(res, "try-error"))
         next

      delpred[i]  <- res$beta
      vdelpred[i] <- res$vb

   }

   if (progbar)
      pbapply::closepb(pbar)

   resid <- x$yi.f - delpred
   resid[abs(resid) < 100 * .Machine$double.eps] <- 0
   #resid[abs(resid) < 100 * .Machine$double.eps * median(abs(resid), na.rm=TRUE)] <- 0 ### see lm.influence
   seresid <- sqrt(x$vi.f + vdelpred)
   stresid <- resid / seresid

   #########################################################################

   if (na.act == "na.omit") {
      out <- list(resid=resid[x$not.na.yivi], se=seresid[x$not.na.yivi], z=stresid[x$not.na.yivi])
      out$slab <- x$slab[x$not.na.yivi]
   }

   if (na.act == "na.exclude" || na.act == "na.pass") {
      out <- list(resid=resid, se=seresid, z=stresid)
      out$slab <- x$slab
   }

   if (na.act == "na.fail" && any(!x$not.na.yivi))
      stop(mstyle$stop("Missing values in results."))

   out$digits <- digits

   if (.isTRUE(ddd$time)) {
      time.end <- proc.time()
      .print.time(unname(time.end - time.start)[3])
   }

   class(out) <- "list.rma"
   return(out)

}
wviechtb/metafor documentation built on March 11, 2024, 11:45 a.m.