[R] Sweave - problems with underscores in variable names...

[Neil Shephard]

Hi all,

I've just started using the Friedrich Leisch's Sweave package to
generate LaTeX reports with results of my analyses embedded as
required.

I've encountered a bit of a problem though in the processing of the
resulting *.tex file that is as far as I can tell, down to the fact
that my variable names have underscores ('_') in their names.

The relevant section of code is....

 <<missing_data,echo=false,results=tex>>=
## Lists observations with missing data
miss_1431 <- subset(gen, PPARG1.2_1431GA == "", select=
c(AAA_ID,PPARG1.2_1431GA))
xtable(miss_1431, caption="Missing data for PPARG1.2-1431GA")
miss_p12a <- subset(gen, PPARG2_P12A_CG == "", select= c(AAA_ID,PPARG2_P12A_CG))
xtable(miss_p12a, caption="Missing data for PPARG2-P12A_CG")

@

and the variables in my data set have the following names...

> names(gen)
[1] "AAA_ID"          "OPN_1083AG"      "OPN_1239AC"      "OPN_282TC"
[5] "OPN_750CT"       "OPN_443CT"       "PPARG1.2_1431GA" "PPARG2_P12A_CG"
[9] "OPG_1181GC"

In tables that are generated have the character after the subscript
subscripted, as opposed to being displayed as desired (see pg 4 of
example output at
http://slack.ser.man.ac.uk/files/genetic_analysis.pdf , please ignore
the table on pg 3, as I said I'm just starting :-).

After googling and searching R-help archives didn't reveal any obvious
problems with this (other than in older versions of R underscores were
not allowed in variable names).

My question is, other than the obvious of renaming my variables, or
manually editing the .tex file that Sweave produces, is there any way
to have variable names with underscores correctly represented in the
resulting tex file?

The error log-file generated when running pdflatex on the .tex file
can be viewed at http://slack.ser.man.ac.uk/files/genetic_analysis.log

Please let me know if I need to provide any more information, and my
thanks in advance,

Neil

> version
         _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    2
minor    2.1
year     2005
month    12
day      20
svn rev  36812
language R

--
"Once, adv. - Enough
Twice, adv. - Once too often"
 - Ambrose Bierce, The Devil's Dictionary

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