[Rd] Rnw file generated strange symbols in pdf file

[Zhu Wang]

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