Modifying a built-in R function

biplotes <- function(x, ...) UseMethod("biplot")

biplotes <- function(x, ...) UseMethod("biplotes")

japal wrote:

Hello,

Something incredible (at least for me) has happen. Yesterday night I
downloaded biplot.R to edit this function and add new features I wished.
Namely I wanted to plot points belonging to different groups using
different colors and symbols. I identified which part of the original code
I had to modify. Then, I rename biplot by biplotes and executing
biplotes(x), being x a princomp class object, the function did what I
wanted.

The problem is that today I type exactly the same (after sourcing my
script file incluiding biplotes) but  biplotes(x) execute the original
biplot function. Also, if I invoke any of the new arguments I wrote in the
code then multiple warnings messages are displayed. I don't understand
what is the problem. Yesterday it works perfectly. Why R does not execute
my code and call the original biplot function?

Thanks in advance,
Javier.

Sorry, I did not show the code: (I have highlighted in bold the changes)

***********************************

biplotes <- function(x, ...) UseMethod("biplot")

biplot.default <-
   function(x, y, color="blue", char=1, var.axes = TRUE, col, cex =
rep(par("cex"), 2),
        xlabs = NULL, ylabs = NULL, expand=1, xlim = NULL, ylim = NULL,
        arrow.len = 0.1,
            main = NULL, sub = NULL, xlab = NULL, ylab = NULL, ...)
{
   n <- nrow(x)
   p <- nrow(y)
   if(missing(xlabs)) {
   xlabs <- dimnames(x)[[1L]]
   if(is.null(xlabs)) xlabs <- 1L:n
   }
   xlabs <- as.character(xlabs)
   dimnames(x) <- list(xlabs, dimnames(x)[[2L]])
   if(missing(ylabs)) {
   ylabs <- dimnames(y)[[1L]]
   if(is.null(ylabs)) ylabs <- paste("Var", 1L:p)
   }
   ylabs <- as.character(ylabs)
   dimnames(y) <- list(ylabs, dimnames(y)[[2L]])

   if(length(cex) == 1L) cex <- c(cex, cex)
   if(missing(col)) {
   col <- par("col")
   if (!is.numeric(col)) col <- match(col, palette(), nomatch=1L)
   col <- c(col, col + 1L)
   }
   else if(length(col) == 1L) col <- c(col, col)


biplot.princomp <- function(x, choices = 1L:2, scale = 1, pc.biplot=FALSE,
...)
{
   if(length(choices) != 2) stop("length of choices must be 2")
   if(!length(scores <- x$scores))
   stop(gettextf("object '%s' has no scores", deparse(substitute(x))),
            domain = NA)
   lam <- x$sdev[choices]
   if(is.null(n <- x$n.obs)) n <- 1
   lam <- lam * sqrt(n)
   if(scale < 0 || scale > 1) warning("'scale' is outside [0, 1]")
   if(scale != 0) lam <- lam^scale else lam <- 1
   if(pc.biplot) lam <- lam / sqrt(n)
   biplot.default(t(t(scores[, choices]) / lam),
          t(t(x$loadings[, choices]) * lam), ...)
   invisible()
}

   unsigned.range <- function(x)
       c(-abs(min(x, na.rm=TRUE)), abs(max(x, na.rm=TRUE)))
   rangx1 <- unsigned.range(x[, 1L])
   rangx2 <- unsigned.range(x[, 2L])
   rangy1 <- unsigned.range(y[, 1L])
   rangy2 <- unsigned.range(y[, 2L])

   if(missing(xlim) && missing(ylim))
   xlim <- ylim <- rangx1 <- rangx2 <- range(rangx1, rangx2)
   else if(missing(xlim)) xlim <- rangx1
   else if(missing(ylim)) ylim <- rangx2
   ratio <- max(rangy1/rangx1, rangy2/rangx2)/expand
   on.exit(par(op))
   op <- par(pty = "s")
   if(!is.null(main))
       op <- c(op, par(mar = par("mar")+c(0,0,1,0)))
   plot(x, type = "p", xlim = xlim, ylim = ylim,
   col = color,pch=char,cex=0.75, #color, s?mbolo y tama?os de los puntos
   xlab = xlab, ylab = ylab, sub = sub, main = main, ...)

   par(new = TRUE)
   plot(y, axes = FALSE, type = "n", xlim = xlim*ratio, ylim = ylim*ratio,
    xlab = "", ylab = "", col = col[1L], ...)
#    axis(3, col = col[2L], ...)
#    axis(4, col = col[2L], ...)
#    box(col = col[1L])
   text(y, labels=ylabs, cex = 0.9, col = "grey32", ...)
   if(var.axes)
   arrows(0, 0, y[,1L] * 0.8, y[,2L] * 0.8,
   col = "grey32", #Arrow color
   length=0.07)
   invisible()
}

*********************************

Note that the problem is solved if (after sourcing the R script incluiding
biplotes function to the current R session) I only copy-paste the
biplot.princomp function into the R console. After this, biplotes apply my
changes correctly, without invoke the original biplot function. But I think
this is only a trick and not the suitable way.

Thanks again.

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