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Problems reading bibtex file with special characters and math in authors/titles

Open ekstroem opened this issue 3 years ago • 0 comments

I'm trying to read in and format a BibTex file that contains a bunch of references. However, some of the entries are not parsed correctly when they are read in. I've browsed the repository, and it might be the same problem as #66 which in turn seems to point back to the bibtex package. So ... maybe it isn't a problem with RefManageR per se but I stumbled upon it using this package.

In my .bib file I have this entry

@ARTICLE{lind:etal:2009,
  author = {Casper Lindegaard and Dorte V{\aa}beng{\aa}rd and Mogens Christophersen and Claus Thorn Ekstr{\o}m and Julie Fjeldborg},
  year = 2009,
  title = {Evaluation of pain and inflammation associated with hot iron branding and microchip transponder injection in horses},
  journal = {American Journal of Veterinary Research},
  pages = {840--847}
}

RefManageR::ReadBib() reads in the file without any complaints, but if I print the entry then I see that some the LaTeX input has been messed up. In particular, the {\o} has been correctly parsed but the {\{aa} has not. Now, BibTeX can be a little ... rigid ... in its input, but using, say, V\aa bengaard doesn't help with anything.

> bib[62]
Lindegaard, Casper, Dorte V\aabeng\aard, Mogens Christophersen, Claus Thorn Ekstrøm, and Julie Fjeldborg (2009). “Evaluation of pain and
inflammation associated with hot iron branding and microchip transponder injection in horses”. In: _American Journal of Veterinary Research_, pp.
840-847.
Warning messages:
1: lind:etal:2009: unknown macro '\aabeng' 
2: lind:etal:2009: unknown macro '\aard' 

If I look at the stuff in the R object then I can see why the LaTeX commands might be messed up

> bib[62]$author
[1] "Casper Lindegaard"     "Dorte V\\aabeng\\aard" "Mogens Christophersen" "Claus Thorn Ekstrøm"   "Julie Fjeldborg"

Now for this entry

@ARTICLE{niel:hans:echw:etal:2003,
  author = {Eva-Maria D. Nielsen and Lars Hansen and S{\o}ren Echwald and
            Thomas Drivsholm and Knut Borch-Johnsen and
            Claus Thorn Ekstr{\o}m and  Torben Hansen and O. Pedersen},
  year = 2003,
  title = {Evidence for an association between the {Leu$^{162}$Val} polymorphism of the {PPAR$\alpha$} gene and decreasing fasting serum triglyceride levels in glucose subjects},
  journal = {Pharmacogenetics},
  volume = 13,
  pages = {417--423}
}

then I get

> bib[66]
Nielsen, Eva-Maria D, Lars Hansen, Søren Echwald, Thomas Drivsholm, Knut Borch-Johnsen, Claus Thorn Ekstrøm, Torben Hansen, and O. Pedersen (2003).
“Evidence for an association between the Leu $^162$Val polymorphism of the PPAR $\alpha$ gene and decreasing fasting serum triglyceride levels in
glucose subjects”. In: _Pharmacogenetics_ 13, pp. 417-423.
Warning message:
niel:hans:echw:etal:2003: unknown macro '\alpha' 

I think (?) that this might be a different error caused by a mess-up between latex backslashes and R string backslashes but I'm not sure. In any case the title seems to be read correctly

> bib[66]$title
[1] "Evidence for an association between the {Leu $^{162}$Val} \n           polymorphism of the {PPAR $\\alpha$} gene and decreasing fasting \n           serum triglyceride levels in glucose subjects"

Is there something that I can do to easily circumvent these issues? Besides digging deep into the source code?

Thank you for a nice package

ekstroem avatar Oct 15 '20 14:10 ekstroem