[R] How to add error bars to plot(x,y)in R?

[Dirk Eddelbuettel]

  "Ming" == mingliz2  <mingliz2 at netscape.net> writes:
  Ming>  Dear R Experts, Is there a way in R to add an error bar (say in the
  Ming> y direction) for each data point?

This is a FAQ. Here is but one reply from the mailing list.

Dirk

   To: Baruch P Feldman <baruchf at mit.edu>
   cc: <r-help at stat.math.ethz.ch>
   Subject: Re: [R] Help with plotting error bars in R
   Date: Mon, 16 Apr 2001 15:29:07 -0400 (EDT)
   Status: O
   Content-Length: 4307
   Lines: 108
   
   
     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.
   > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
   > r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
   > Send "info", "help", or "[un]subscribe"
   > (in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
   > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
   >
   
   -- 
   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
    

-- 
Good judgment comes from experience; experience comes from bad judgment. 
							    -- F. Brooks
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._