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How to avoid "$ operator is invalid for atomic vectors" in R

Using some versions of R (2.8 and 2.9) you sometimes get the mystifying error message "$ operator is invalid for atomic vectors" . This can happen even if the R code you are running worked in earlier versions.

This may be due to inputting data as matrix data rather than a dataframe in R. You can so this conversion easily using the command as.data.frame.

% matrix data
% converted to dataframe format

This advice is presented in fuller detail here.