Just as an update on encoding (which may or may not be of interest). I
changed the read.csv command for three .csv files I was reading to specify
the encoding to be
encoding="CP1252"
and all 3 files were read in without problems on linux. Last night I
swapped the analysis back on to my windows machine, and one of the reads
stopped part way through with a message about illegal characters. I
checked around where the read stopped but couldn't see what the problem
was. Dropping the encoding argument to "file" worked around the problem.
I now have an if then else which tests what system I am on. Painful but at
least it is system independent.
Thanks again
David
On Tue, 22 Jan 2008, Prof Brian Ripley wrote:
> On Wed, 23 Jan 2008, David Scott wrote:
>
>> On Tue, 22 Jan 2008, Prof Brian Ripley wrote:
>>
>>> On Wed, 23 Jan 2008, David Scott wrote:
>>>
>>>>
>>>> I have encountered a problem with reading a .csv file on a linux box. I
>>>> can read the file on my windows machine (under XP) but on the linux box
>>>> it
>>>> gives :
>>>>
>>>>> patients <- read.csv("../Patients.csv", header = FALSE,
>>>> + col.names = patientsNames)
>>>> Error in type.convert(data[[i]], as.is = as.is[i], dec = dec,
>>>> na.strings = character(0)) :
>>>> invalid multibyte string
>>>> Calls: read.csv -> read.table -> type.convert
>>>> Execution halted
>>>>
>>>> I am running R 2.6.1 on both machines. I tried on another linux box
>>>> running 2.5.1 and got the same problem
>>>>
>>>> I am guessing it is something to do with the character encoding. On the
>>>> linux box I have
>>>>
>>>> LANG=en_US.UTF-8
>>>
>>> So what encoding is the .csv file in? Consider the example at the end of
>>> ?file
>>>
>>> ## examples of use of encodings
>>> cat(x, file = file("foo", "w", encoding="UTF-8"))
>>> # read a 'Windows Unicode' file including names
>>> A <- read.table(file("students", encoding="UCS-2LE"))
>>>
>>> and adapt accordingly (encoding = "CP1252" is the most likely value if
>>> this works in English-language Windows).
>>>
>>
>>
>> Thanks Brian for the super-quick, super-helpful reply. The encoding you
>> suggested worked.
>>
>> I found a workaround myself too---I guessed that some plus/minus signs
>> might be the problem and replaced them and could read in the file.
>> That is just a kludge so I am using the encoding specification.
>>
>> I am a total dunce when it comes to encodings though. How do you find the
>> encoding of a file?
>
> You ask the person who gave it to you. You can't in general tell, and e.g.
> ISO-8859-1 and ISO-8859-2 are only distinguishable by someone who can read
> the contents (if it is a human language). If you have just the odd symbol
> (e.g. degree sign or plus/minus) you can be completely stuck.
>
> 'file' on Linux can usually guess if a file is UTF-8 or ISO-8859-?, but not
> of course what ? is. But guesses are based on statistical patterns and are
> good for text but not so good for data.
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
>
_________________________________________________________________
David Scott Department of Statistics, Tamaki Campus
The University of Auckland, PB 92019
Auckland 1142, NEW ZEALAND
Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000
Email: [EMAIL PROTECTED]
Graduate Officer, Department of Statistics
Director of Consulting, Department of Statistics
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