When I read in csv files to r the requesting dataframe has very different dimensions than I see when I open the file in excel or notepad and the column heading is labeled as "ÿþA". What does this mean?
The file you are reading is using an UTF-16 or UTF-32 encoding (with a BOM), and the r read.csv function has not been informed correctly.
As Karsten suggests you should use the fileEncoding parameter to specify the correct encoding, which I suspect should be "UTF-16LE".
Here is what the R Studio documentation states about encoding:
The encoding of the input/output stream of a connection can be specified by name in the same way as it would be given to iconv: see that help page for how to find out what encoding names are recognized on your platform. Additionally, "" and "native.enc" both mean the ‘native’ encoding, that is the internal encoding of the current locale and hence no translation is done.
Re-encoding only works for connections in text mode: reading from a connection with re-encoding specified in binary mode will read the stream of bytes, but mixing text and binary mode reads (e.g. mixing calls to readLines and readChar) is likely to lead to incorrect results.
The encodings "UCS-2LE" and "UTF-16LE" are treated specially, as they are appropriate values for Windows ‘Unicode’ text files. If the first two bytes are the Byte Order Mark 0xFFFE then these are removed as some implementations of iconv do not accept BOMs. Note that whereas most implementations will handle BOMs using encoding "UCS-2" and choose the appropriate byte order, some (including earlier versions of glibc) will not. There is a subtle distinction between "UTF-16" and "UCS-2" (see http://en.wikipedia.org/wiki/UTF-16/UCS-2: the use of surrogate pairs is very rare so "UCS-2LE" is an appropriate first choice.
As from R 3.0.0 the encoding "UTF-8-BOM" is accepted for reading and will remove a Byte Order Mark if present (which it often is for files and webpages generated by Microsoft applications). If it is required (it is not recommended) when writing it should be written explicitly, e.g. by writeChar("\ufeff", con, eos = NULL) or writeBin(as.raw(c(0xef, 0xbb, 0xff)), binary_con)
Requesting a conversion that is not supported is an error, reported when the connection is opened. Exactly what happens when the requested translation cannot be done for invalid input is in general undocumented. On output the result is likely to be that up to the error, with a warning. On input, it will most likely be all or some of the input up to the error.
It may be possible to deduce the current native encoding from Sys.getlocale("LC_CTYPE"), but not all OSes record it.
And here is what Wiki states on the BOM:
The byte order mark (BOM) is a Unicode character used to signal the endianness (byte order) of a text file or stream. It is encoded at U+FEFF byte order mark (BOM). BOM use is optional, and, if used, should appear at the start of the text stream. Beyond its specific use as a byte-order indicator, the BOM character may also indicate which of the several Unicode representations the text is encoded in.1
Because Unicode can be encoded as 16-bit or 32-bit integers, a computer receiving these encodings from arbitrary sources needs to know which byte order the integers are encoded in. The BOM gives the producer of the text a way to describe the text stream's endianness to the consumer of the text without requiring some contract or metadata outside of the text stream itself. Once the receiving computer has consumed the text stream, it presumably processes the characters in its own native byte order and no longer needs the BOM. Hence the need for a BOM arises in the context of text interchange, rather than in normal text processing within a closed environment.