<snip>


I think I have identified the problem such that when I identify the
structure of some of the files that I am reading in, columns are labeled as
"Factors".  In other files, the same columns are labeled as numeric
values.  Is there a way to assign the data structure to these columns in the
dataframe as they are being read in?  Any other suggestions to why I am
getting this error is appreciated.


Yes, as ?read.table describes, see the colClasses argument.

However, you should investigate why read.table wants to treat these particular columns as factors. If they are indeed simply consisting of all numeric values, there shouldn't be a problem. The fact that they are coming out as factors raises a flag to me ...

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