R help - Mar 2009 - Variable scope.

I have a question on scope/reference/value type of variables with 'R'.

The issue cam up first when I look at the arima code.

I see code like:

    myupARIMA <- function(mod, phi, theta) {
. . . .
                           mod
    }

Then 

armafn <- function(p, trans) {
. . . .
        Z <- upARIMA(mod, trarma[[1]], trarma[[2]])
. . . .
        res <- .Call(R_ARIMA_Like, x, Z$phi, Z$theta, Z$Delta, 
            Z$a, Z$P, Z$Pn, as.integer(0), FALSE)
. . . . 
}

The question is that ARIMA_Like will make changes to the arrays Z$P etc. Since
upARIMA essentially returns 'mod' are changes to the arrays passed as
Z$... to ARUINA_Like refkected in the original 'mod'? Or another way of
phrasing the question is 'Z' a reference variable? Are the members such
as Z$a also passed as reference hence changes to Z$a should also be seen in
mod$a? In the arima code the references to x and mod seem to be essentially
global variables as armafn is 'nested' in arima. Will changes to x also
be reflected in the original x? (Like x <- x - (xreg %*% par[narma +
(1:ncxreg)))

Thank you.

Kevin