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# $Id: plotCI.R 1318 2009-05-08 21:56:38Z warnes $
plotCI <- function (x,
y = NULL,
uiw,
liw = uiw,
ui,
li,
err='y',
ylim=NULL,
xlim=NULL,
type="p",
col=par("col"),
barcol=col,
pt.bg = par("bg"),
sfrac = 0.01,
gap=1,
lwd=par("lwd"),
lty=par("lty"),
labels=FALSE,
add=FALSE,
xlab,
ylab,
minbar,
maxbar,
...
)
{
if (is.list(x)) {
y <- x$y
x <- x$x
}
if(invalid(xlab))
xlab <- deparse(substitute(x))
if(invalid(ylab))
{
if(is.null(y))
{
xlab <- ""
ylab <- deparse(substitute(x))
}
else
ylab <- deparse(substitute(y))
}
if (is.null(y)) {
if (is.null(x))
stop("both x and y NULL")
y <- as.numeric(x)
x <- seq(along = x)
}
if(err=="y")
z <- y
else
z <- x
if(invalid(uiw))
uiw <- NA
if(invalid(liw))
liw <- NA
if(invalid(ui))
ui <- z + uiw
if(invalid(li))
li <- z - liw
if(!invalid(minbar))
li <- ifelse( li < minbar, minbar, li)
if(!invalid(maxbar))
ui <- ifelse( ui > maxbar, maxbar, ui)
if(err=="y")
{
if(is.null(ylim))
ylim <- range(c(y, ui, li), na.rm=TRUE)
if(is.null(xlim))
xlim <- range( x, na.rm=TRUE)
}
else if(err=="x")
{
if(is.null(xlim))
xlim <- range(c(x, ui, li), na.rm=TRUE)
if(is.null(ylim))
ylim <- range( x, na.rm=TRUE)
}
if(!add)
{
if(invalid(labels) || labels==FALSE )
plot(x, y, ylim = ylim, xlim=xlim, col=col,
xlab=xlab, ylab=ylab, ...)
else
{
plot(x, y, ylim = ylim, xlim=xlim, col=col, type="n",
xlab=xlab, ylab=ylab, ...)
text(x, y, label=labels, col=col, ... )
}
}
myarrows <- function(...) arrows(...)
# works only using R!!
# else
# myarrows <- function(x1,y1,x2,y2,angle,code,length,...)
# {
# segments(x1,y1,x2,y2,open=TRUE,...)
# if(code==1)
# segments(x1-length/2,y1,x1+length/2,y1,...)
# else
# segments(x2-length/2,y2,x2+length/2,y2,...)
# }
if(err=="y")
{
if(gap!=FALSE)
gap <- strheight("O") * gap
smidge <- par("fin")[1] * sfrac
# draw upper bar
if(!is.null(li))
myarrows(x , li, x, pmax(y-gap,li), col=barcol, lwd=lwd,
lty=lty, angle=90, length=smidge, code=1)
# draw lower bar
if(!is.null(ui))
myarrows(x , ui, x, pmin(y+gap,ui), col=barcol,
lwd=lwd, lty=lty, angle=90, length=smidge, code=1)
}
else
{
if(gap!=FALSE)
gap <- strwidth("O") * gap
smidge <- par("fin")[2] * sfrac
# draw left bar
if(!is.null(li))
myarrows(li, y, pmax(x-gap,li), y, col=barcol, lwd=lwd,
lty=lty, angle=90, length=smidge, code=1)
if(!is.null(ui))
myarrows(ui, y, pmin(x+gap,ui), y, col=barcol, lwd=lwd,
lty=lty, angle=90, length=smidge, code=1)
}
## _now_ draw the points (to avoid having lines drawn 'through' points)
points(x, y, col = col, lwd = lwd, bg = pt.bg, type = type, ...)
invisible(list(x = x, y = y))
}
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