[R] Modifying a built-in R function

[japal]

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, símbolo y tamaños 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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