[R] Connecting lines across missing data points, xyplot

From: David Afshartous <dafshartous_at_med.miami.edu>
Date: Thu, 26 Jun 2008 10:26:15 -0400

All,

I have data across 5 time points that I am graphing via xyplot, along with error bars. For one of the variables I have missing data for two of the time points. The code below is okay but I can't seem to get the lines to connect across the missing time points. Does anyone now how to rectify this?

Cheers,
David Afshartous

library(lattice)
## the data

junk = data.frame(
Visit = as.factor(rep(seq(1,5), 2)),
Drug = rep(c("D", "P"), each = 5),
Aldo = c(13, NA, NA, 15, 14, 12, NA, NA, 14, 13),

SE.Aldo = c(3,  NA, NA, 3, 3, 2, NA, NA, 2, 2),
lower.ci.Aldo = c(10, NA, NA, 12, 11,  10,NA,  NA, 12, 11),
upper.ci.Aldo = c(16, NA, NA, 18, 17, 14, NA, NA, 16, 15)
)

## functions for the error bars

prepanel.ci <- function(x, y, ly, uy, subscripts, ...) {

    x <- as.numeric(x)
    ly <- as.numeric(ly[subscripts])
    uy <- as.numeric(uy[subscripts])
    list(ylim = range(y, uy, ly, finite = TRUE)) } panel.ci <- function(x, y, ly, uy, subscripts, pch = 16, ...) {

    x <- as.numeric(x)
    y <- as.numeric(y)
    ly <- as.numeric(ly[subscripts])
    uy <- as.numeric(uy[subscripts])
    panel.arrows(x, ly, x, uy, col = "black",

                 length = 0.25, unit = "native",
                 angle = 90, code = 3)

    panel.xyplot(x, y, pch = 16, ...)}

## the plot, but visit 1 not connected to visit 4
xyplot(Aldo ~ as.numeric(Visit), xlab="Visit", ylab="Aldo",

        groups=Drug,
        data=junk,
        ly = junk$lower.ci.Aldo,
        uy = junk$upper.ci.Aldo,
        prepanel = prepanel.ci,
        panel = panel.superpose,
        panel.groups = panel.ci,
        type="b",
        auto.key = list(space = "top",  text = c( "D","P"), points = FALSE,
lines = TRUE, columns=2),
par.settings = list(superpose.line = list(lty = c(1,5), col=c('black', 'black') ) ) )

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