R devel - Jan 2012 - Rnw file generated strange symbols in pdf file

Hello,
 
I found my Rnw file generated strange symbols in pdf file. For instance, on page
4 of the following file,
 
http://cran.r-project.org/web/packages/cts/vignettes/kf.pdf
 
you can see Belcher et~al on line 2, and Figure~1 on line 5. The symbol ~ should
not appear in the pdf file although the symbol was in the original Rnw file
(something like Figure~\ref{...}, section~\ref{...}). On page 1, the symbol ~
also appears after Keywords but in my original Rnw file I have
\Keywords{continuous time autoregressive model, state space model, Kalman
filter, Kalman smoothing, \proglang{R}}.
 
The symbol ~ didn't appear in the generated pdf file with the early R
version before 2.14, if my memory serves me correctly. So what's wrong here
and how to correct it rather than modifying my original Rnw file?
 
Thank you very much.
 
Zhu Wang

Zhu Wang <Zwang <at> ccmckids.org> writes:
> I found my Rnw file generated strange symbols in pdf file. 
> For instance, on page 4 of the following file,
> 
> http://cran.r-project.org/web/packages/cts/vignettes/kf.pdf
> you can see Belcher et~al on line 2, and Figure~1 on line 5. The
> symbol ~ should not appear in the pdf file although the symbol was
> in the original Rnw file (something like Figure~\ref{...},
> section~\ref{...}). On page 1, the symbol ~ also appears after
> Keywords but in my original Rnw file I have \Keywords{continuous
> time autoregressive model, state space model, Kalman filter, Kalman
> smoothing, \proglang{R}}.
 
> The symbol ~ didn't appear in the generated pdf file with the early
> R version before 2.14, if my memory serves me correctly. So what's
> wrong here and how to correct it rather than modifying my original
> Rnw file?
  This has come up before, I'm not sure what the current status is,
not what gets run on CRAN.  I know that if I use texi2pdf on my
(now fairly old) 10.04 version of Ubuntu, I get the 'tilde problem'
if I use texi2pdf but not if I use pdflatex.  If I \usepackage[english]{babel}
the problem also goes away.

References:

http://comments.gmane.org/gmane.comp.lang.r.debian/848

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=534458

http://www2.it.lut.fi/wiki/doku.php/common/latex_hints  says:
If you use both natbib and babel packages, load natbib before babel to
prevent tilde showing up in citations. Loading natbib after babel and
using citep-command will make ?et al.? shown as ?et~al.?.