[R] Help with plotting error bars in R

[ben@zoo.ufl.edu]

  This comes up as a FAQ every so often (it hasn't yet been added to the
official FAQ list), you can find it in the mail archives in several
places.

http://www.R-project.org/nocvs/mail/r-help/2000/0451.html
http://www.R-project.org/nocvs/mail/r-help/2000/2289.html
http://www.R-project.org/nocvs/mail/r-help/2000/3326.html

  (plus a whole recent discussion of whether to include a plotCI function
in the R base, or just to tell people how to do what they want using
arrows() or segments())

  Here's the most recent version of my function:

plotCI <- function (x, y = NULL, uiw, liw = uiw, aui=NULL, ali=aui,
                    err="y", ylim=NULL, sfrac = 0.01, gap=0, add=FALSE,
                    col=par("col"), lwd=par("lwd"), slty=par("lty"), xlab=NULL,
                    ylab=NULL, ...)  {
## originally from Bill Venables, R-list
  if (is.list(x)) {
    y <- x$y
    x <- x$x
  }
  if (is.null(y)) {
    if (is.null(x))
      stop("both x and y NULL")
    y <- as.numeric(x)
    x <- seq(along = x)
  }
  if (missing(xlab)) xlab <- deparse(substitute(x))
  if (missing(ylab)) ylab <- deparse(substitute(y))
  if (missing(uiw)) {  ## absolute limits
    ui <- aui
    li <- ali
  }
  else {  ## relative limits
    if (err=="y") z <- y else z <- x
    ui <- z + uiw
    li <- z - liw
  }
  if (is.null(ylim)) ylim <- range(c(y, ui, li), na.rm=TRUE)
  if (add) {
    points(x, y, col=col, lwd=lwd, ...)
  } else {
    plot(x, y, ylim = ylim, col=col, lwd=lwd, xlab=xlab, ylab=ylab, ...)
  }
  if (gap==TRUE) gap <- 0.01  ## default gap size
  ul <- c(li, ui)
  if (err=="y") {
    gap <- rep(gap,length(x))*diff(par("usr")[3:4])
#    smidge <- diff(par("usr")[1:2]) * sfrac
    smidge <- par("fin")[1] * sfrac
#    segments(x , li, x, pmax(y-gap,li), col=col, lwd=lwd, lty=slty)
#    segments(x , ui, x, pmin(y+gap,ui), col=col, lwd=lwd, lty=slty)
    arrows(x , li, x, pmax(y-gap,li), col=col, lwd=lwd, lty=slty, angle=90, length=smidge, code=1)
    arrows(x , ui, x, pmin(y+gap,ui), col=col, lwd=lwd, lty=slty, angle=90, length=smidge, code=1)
    ## horizontal segments
#    x2 <- c(x, x)
#    segments(x2 - smidge, ul, x2 + smidge, ul, col=col, lwd=lwd)
  }
  else if (err=="x") {
    gap <- rep(gap,length(x))*diff(par("usr")[1:2])
    smidge <- par("fin")[2] * sfrac
#    smidge <- diff(par("usr")[3:4]) * sfrac
    arrows(li, y, pmax(x-gap,li), y, col=col, lwd=lwd, lty=slty, angle=90, length=smidge, code=1)
    arrows(ui, y, pmin(x+gap,ui), y, col=col, lwd=lwd, lty=slty, angle=90, length=smidge, code=1)
    ## vertical segments
#    y2 <- c(y, y)
#    segments(ul, y2 - smidge, ul, y2 + smidge, col=col, lwd=lwd)
  }
  invisible(list(x = x, y = y))
}

On Mon, 16 Apr 2001, Baruch P Feldman wrote:

> Hi,
>
> I'm sorry to send email to everyone on this list, but I have a simple question
> which is bothering me and I can't seem to figure out the correct answer.  I
> just downloaded R and I'm trying to reproduce some simple analysis I've done
> on other packages.  In particular, if I have a vector of experimental values
> and a vector of their uncertainties, is there a way to plot the values using
> the uncertainties as error bars?  Other than this one problem R so far seems to
> be a very good package.
>
> I'd greatly appreciate it if someone could reply to my email directly.
>
> Thank you.
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-- 
318 Carr Hall                                bolker at zoo.ufl.edu
Zoology Department, University of Florida    http://www.zoo.ufl.edu/bolker
Box 118525                                   (ph)  352-392-5697
Gainesville, FL 32611-8525                   (fax) 352-392-3704


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