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I’ve often selected columns or rows of a data frame using grep or which, based on some property. That is inherently sound, but the trouble comes when you wish to remove rows or columns based on that grep or which call, e.g.,

dat <- dat[,-grep('\\.1', names(dat))]


which would remove columns with a .1 in the name. This is fine the first time around, but if you forget and re-run the code, grep('\\.1',names(dat)) gives a vector of length 0, and hence dat becomes a data.frame with 0 columns. The function which also has similar pitfalls, as demonstrated in a recent R-help posting by David Winsemius. I find a more reliable method is to do

dat <- dat[,setdiff(1:ncol(dat),grep('\\.1',names(dat)))]


which will always give the right number of columns. Other suggestions for getting around this issue are welcomed in the comments.