> the "unhelpful" column are the row names. They are considered an
> important part of a data frame and therefore the default (row.names =
> TRUE) is to not lose them (as there is no way back once you do). If you don't
> want to preserve the row names you can simply set row.names=FALSE.
Please run the reproducible example provided.
When you do, you will see that write.csv writes an unnecessary empty header
field ("") over the row names column. This makes the number of header fields
equal to the number of columns _including_ row names. That causes the original
row names to be read as data by read.csv, following the rule that the number of
header fields determines whether row names are present. read.csv accordingly
assumes that the former row names are unnamed data, calls the unnamed row names
column "X" (or X.1 etc if X exists) and then adds new, default, row names
_instead of the original row names written by write.csv_.
That's not helpful.
By contrast read.table correctly reads the first entry in each row as a row
name when the number of header fields is one less than the number of data
columns. write.table includes row names as row names _without a header field_,
so a file written with write.table is correctly formatted for read.table to
interpret the first data field as a row name.
I think it would be more sensible if write.csv did the same as write.table when
row.names=TRUE - as it is, by default.
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