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.
### 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$gr, cor, use=3D"complete", method=3D"pearson") # This induces error by(testdata[,c("aa", "bb")], testdata$gr, cor, use=3D"complete", method=3D"spearman") 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: mlmRev lme4 Matrix lattice=20 "0.995-1" "0.99875-2" "0.99875-3" "0.15-4"=20 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel