[R] Confidence interval bars on Lattice barchart with groups

[Deepayan Sarkar]

On 6/25/05, Tim Churches <tchur at optushome.com.au> wrote:
> I am trying to add confidence (error) bars to lattice barcharts (and
> dotplots, and xyplots). I found this helpful message from Deepayan
> Sarkar and based teh code below on it:
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/50299.html
> 
> However, I can't get it to work with groups, as illustrated. I am sure I
> am missing something elementary, but I am unsure what.
> 
> Using R 2.1.1 on various platforms. I am aware of xYplot in the Hmisc
> library but would prefer to avoid any dependency on a non-core R
> library, if possible.
> 
> Tim C
> 
> ##################################################################
> # set up dummy test data
> testdata <- data.frame(
> dsr=c(1,2,3,4,5,6,7,8,9,10,0,1,2,3,4,5,6,7,8,9,
>       2,3,4,5,6,7,8,9,10,11,3,4,5,6,7,8,9,10,11,12),
> year=as.factor(c(1998,1998,1998,1998,1998,1998,1998,1998,1998,1998,
>                  1999,1999,1999,1999,1999,1999,1999,1999,1999,1999,
>                  2000,2000,2000,2000,2000,2000,2000,2000,2000,2000,
>                  2001,2001,2001,2001,2001,2001,2001,2001,2001,2001)),
> geog_area=c('North','South','East','West','Middle',
>             'North','South','East','West','Middle',
>             'North','South','East','West','Middle',
>             'North','South','East','West','Middle',
>             'North','South','East','West','Middle',
>             'North','South','East','West','Middle',
>             'North','South','East','West','Middle',
>             'North','South','East','West','Middle'),
> sex=c('Male','Male','Male','Male','Male',
>       'Female','Female','Female','Female','Female',
>       'Male','Male','Male','Male','Male',
>       'Female','Female','Female','Female','Female',
>       'Male','Male','Male','Male','Male',
>       'Female','Female','Female','Female','Female',
>       'Male','Male','Male','Male','Male',
>       'Female','Female','Female','Female','Female'),
> age=c('Old','Old','Old','Old','Old',
>       'Young','Young','Young','Young','Young',
>       'Old','Old','Old','Old','Old',
>       'Young','Young','Young','Young','Young',
>       'Old','Old','Old','Old','Old',
>       'Young','Young','Young','Young','Young',
>       'Old','Old','Old','Old','Old',
>       'Young','Young','Young','Young','Young'))
> 
> # add dummy lower and upper confidence limits
> testdata$dsr_ll <- testdata$dsr - 0.7
> testdata$dsr_ul <- testdata$dsr + 0.5
> 
> # examine the test data
> testdata
> 
> # check that a normal barchart with groups works OK - it does
> barchart(geog_area ~ dsr | year, testdata, groups=sex, origin = 0)
> 
> # this works as expected, but not sure what teh error messages mean
> with(testdata,barchart(geog_area ~ dsr | year + sex,
>               origin = 0,
>               dsr_ul = dsr_ul,
>               dsr_ll = dsr_ll,
>               panel = function(x, y, ..., dsr_ll, dsr_ul, subscripts) {
>                   panel.barchart(x, y, subscripts, ...)

This is where the warnings are coming from. You are using positional
matching to supply (unnamed) arguments, but the third argument of
panel.barchart is not 'subscripts'. You should use

                  panel.barchart(x, y, subscripts = subscripts, ...)

instead.


>                   dsr_ll <- dsr_ll[subscripts]
>                   dsr_ul <- dsr_ul[subscripts]
>                   panel.segments(dsr_ll,
>                                  as.numeric(y),
>                                  dsr_ul,
>                                  as.numeric(y),
>                                  col = 'red', lwd = 2)}
>               ))
> 
> # no idea what I am doing wrong here, but there is not one bar per
> group... something
> # to do with panel.groups???
> with(testdata,barchart(geog_area ~ dsr | year, groups=sex,
>               origin = 0,
>               dsr_ul = dsr_ul,
>               dsr_ll = dsr_ll,
>               panel = function(x, y, ..., dsr_ll, dsr_ul, subscripts,
> groups) {
>                   panel.barchart(x, y, subscripts, groups, ...)
>                   dsr_ll <- dsr_ll[subscripts]
>                   dsr_ul <- dsr_ul[subscripts]
>                   panel.segments(dsr_ll,
>                                  as.numeric(y),
>                                  dsr_ul,
>                                  as.numeric(y),
>                                  col = 'red', lwd = 2)}
>               ))

panel.groups will not help here, since placing multiple bars side by
side needs specialized calculations, which are done within
panel.barchart. To add bars to these, you will need to reproduce those
calculations.

Things are much easier with dotplot, e.g.:

with(testdata,
     dotplot(geog_area ~ dsr | year,
             groups=sex, pch = 16,
             dsr_ul = dsr_ul,
             dsr_ll = dsr_ll,
             panel.groups =
             function(x, y, ..., 
                      dsr_ll, dsr_ul,
                      subscripts) {
                 dsr_ll <- dsr_ll[subscripts]
                 dsr_ul <- dsr_ul[subscripts]
                 panel.segments(dsr_ll,
                                as.numeric(y),
                                dsr_ul,
                                as.numeric(y),
                                ...)
                 panel.xyplot(x, y, ...)
             }))

Deepayan