This is nothing whatsoever to do with by(), and it is cor, not Cor.
Try
X - cbind(NA, 1:3)
cor(X, use = complete)
cor(X, use = complete, method=spearman)
In short, cor() behaves differently when given a vector of NAs. That's
perfectly reasonable, as the ranks are undefined.
Since
cor(na.omit(X))
Error in cor(na.omit(X)) : 'x' is empty
I would say that consistency requires that both examples give an error.
On Thu, 20 Sep 2007, [EMAIL PROTECTED] wrote:
I posted this on R help, and a few others responded indicating they too
were able to replicate the error as a function of missing data. I
believe this should not be the case and hence and reporting it here.
But you have failed to explain to us why such an example must work: your
'belief' is not relevant here. As the FAQ says, do not report as a bug
something you do not 'know for certain'.
### Code provided on R-Help by Ivar Herfindal
# Simulate data
testdata - cbind.data.frame(gr=3Drep(letters[1:4], each=3D5), =
aa=3Drnorm(20),
bb=3Drnorm(20))
# Introduce some missingness
testdata[1:5, 2] - NA
# This works fine
by(testdata[,c(aa, bb)], testdata$gr, cor, use=3Dcomplete,
method=3Dpearson)
# This induces error
by(testdata[,c(aa, bb)], testdata$gr, cor, use=3Dcomplete,
method=3Dspearman)
Error in FUN(data[x, ], ...) : 'x' is empty
## Alternatively, we can try this
# This works fine
by(testdata[,c('aa', 'bb')], testdata$gr, cor, use=3D'complete',
method=3D'pearson')
## This induces the same error
by(testdata[,c('aa', 'bb')], testdata$gr, cor, use=3D'complete',
method=3D'spearman')
Error in FUN(data[x, ], ...) : 'x' is empty
I am using Windows XP with session info below
Harold Doran
sessionInfo()
R version 2.5.0 (2007-04-23)=20
i386-pc-mingw32=20
locale:
LC_COLLATE=3DEnglish_United States.1252;LC_CTYPE=3DEnglish_United
States.1252;LC_MONETARY=3DEnglish_United
States.1252;LC_NUMERIC=3DC;LC_TIME=3DEnglish_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets
methods base=20
other attached packages:
mlmRevlme4 Matrix lattice=20
0.995-1 0.99875-2 0.99875-30.15-4=20
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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