On 11-08-15 7:48 PM, Denis Chabot wrote:
Le 2011-08-15 ? 19:06, Duncan Murdoch a ?crit :
On 11-08-15 2:42 PM, Denis Chabot wrote:
Hi,
I usually do not give second thought to accented vowels and R handles everything fine thanks to UTF8 being used in my R scripts. But today I have a problem. Accented vowels do not behave properly when they were imported into R using list.files.
Maybe this is because OS X (I'm using 10.6.8) still uses MacRoman for file names, though visually the names seem to have been read correctly into R.
An example is better than words:
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
This does not cause problem:
a = c("1_MO2 crevettes po2crit.Rda", "1_MO2 soles S?te sda.Rda", "1_MO2 turbots po2crit.Rda"); a
[1] "1_MO2 crevettes po2crit.Rda" "1_MO2 soles S?te sda.Rda" "1_MO2 turbots po2crit.Rda"
a2 = gsub(" S?te", "S", a); a2
[1] "1_MO2 crevettes po2crit.Rda" "1_MO2 solesS sda.Rda" "1_MO2 turbots po2crit.Rda"
but if instead of creating the vector within the R script, I read it as a series of file names, the substitution does not work. I am sorry that I cannot make this a reproducible example as it requires the 3 files to exist on your computer, but you could create 3 dummy files having the same names in the directory of your choice.
don = file.path("donn?es/")
b = list.files(path = don, pattern = "1_MO2"); b
[1] "1_MO2 crevettes po2crit.Rda" "1_MO2 soles S?te sda.Rda" "1_MO2 turbots po2crit.Rda"
b2 = gsub(" S?te", "S", b); b2
[1] "1_MO2 crevettes po2crit.Rda" "1_MO2 soles S?te sda.Rda" "1_MO2 turbots po2crit.Rda"
I am puzzled and also "stuck". For now I'll modify the file name, but I need to be able to handle such names at some point.
Any advice?
Possibly your system really is using MacRoman or some other local encoding; in that case, iconv(x, "", "UTF-8") should convert from the local encoding to UTF-8.
I think declaring everything to be UTF8 may be sufficient. When I use list.files(), I see the encoding listed as "unknown", but
x<- list.files()
Encoding(x)<- "UTF-8"
works. However, the iconv() method should be safer.
Duncan Murdoch
Hi Duncan,
iconv() confirmed what I suspected: there was no problem with the encoding of the result of list.files, and if there had been one, the "?" would not have looked like a "?". Therefore, I got nonsense when treating this "?" as MacRoman to be converted into UTF-8:
iconv(b, from="MacRoman", to="UTF-8")
[1] "1_MO2 crevettes po2crit.Rda" "1_MO2 soles Se??te sda.Rda" "1_MO2 turbots po2crit.Rda"
It is not clear however that R considered b to be UTF=8:
Encoding(b)
[1] "unknown" "unknown" "unknown"
so I followed your suggestion:
Encoding(b)<- "UTF-8"
Encoding(b)
[1] "unknown" "UTF-8" "unknown"
but gsub still did not work:
b2 = gsub(" S?te", "S", b); b2
[1] "1_MO2 crevettes po2crit.Rda" "1_MO2 soles S?te sda.Rda" "1_MO2 turbots po2crit.Rda"
I do not know why gsub worked with example "a" but not "b" in the example shown in my original message. Strange and frustrating.
Unicode sometimes gives different ways to encode what is rendered as the same character (e.g. letter + accent versus accented letter). I think (see below) the OS uses one convention, but R chooses the other when it parses your text.
Cut and paste did just work for me, in a version of R 2.13.0 Patched which predates 2.13.1 by a few weeks; I'm not up to date on my Mac:
[1] "1_MO2 soles S?te sda.Rda"
[1] "1_MO2 soles XXXX sda.Rda"
In the second line, I didn't try to type the pattern containing S?te, I just cut and pasted it from the printed version of x.
One other possibility (and perhaps it's the best one, if your substitutions are all so simple) is to use the useBytes=TRUE option to gsub. You can use charToRaw to see the bytes in a string, to make sure they are what you expect.
When I do that, I see that the ? really is handled differently in the two cases:
charToRaw("S?te") # cut and paste from list.files() output
charToRaw("S?te") # entered on the keyboard
[1] 53 c3 a8 74 65
So your solution is ugly: you'll need to code all your substitutions twice (or more!) to handle all the possible ways the same letter could be encoded. Or maybe iconv() or some other function has an option to normalize the encoding. (I've just read some more about the issue in http://en.wikipedia.org/wiki/Unicode_equivalence; normalization is what you want to do, but I don't know how to do it.)
Duncan Murdoch