R help - Jun 2008 - Connecting lines across missing data points, xyplot

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') ) )        )

Maybe approx() will work? 
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of David Afshartous
> Sent: Thursday, June 26, 2008 10:26 AM
> To: r-help at r-project.org
> Subject: [R] Connecting lines across missing data points, xyplot
> 
> 
> 
> 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') ) )        )
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

On 6/26/08, David Afshartous <dafshartous at med.miami.edu>
wrote:
>
>
>  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?
Well, I don't think joining lines ignoring NA-s would be a good idea
in general. If you want that behaviour, you need to omit the NA's,
either using

  junk <- na.omit(junk)

before the xyplot call, or add

  subset = !is.na(Aldo),

to the xyplot call.

-Deepayan
>
>  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') ) )        )
>
>  ______________________________________________
>  R-help at r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>

Just had to comment that I thought this question was unintentionally 
funny,  seeing as many of us have gone thru a lot of pain to force Excel 
NOT to join lines across NA-type points in our data.

Back to the subject:  if you use is.na(),  just be careful to remove the 
corresponding values in the x-data as well as the y-data :-) .  Probably 
mucking with something like
  >if (y[j]=NA) y[j]<-approx({local x and y data fit})