[R] bibtex::read.bib -- extracting bibentry keys

[Achim Zeileis]

On Mon, 6 Aug 2012, Michael Friendly wrote:

> I have two versions of a bibtex database which have gotten badly out of 
> sync. I need to find find all the entries in bib2 which are not 
> contained in bib1, according to their bibtex keys. But I can't figure 
> out how to extract a list of the bibentry keys in these databases.

read.bib() returns a "bibentry" object so you can simply do this as usual
for "bibentry" objects with $key:

x <- read.bib(...)
x$key

or maybe

unlist(x$key)

Whatever is more convenient for you. See ?bibentry for more details.

> A minor question: Is there someway to prevent read.bib from ignoring 
> entries that do not contain all required fields?

Also not really an issue with read.bib itself. read.bib() wants to return 
a "bibentry" object but bibentry() just allows to create objects that are 
valid BibTeX, i.e., have all required fields.

> A suggestion: it would be nice if bibtex provided some extractor functions 
> for bibentry fields.

So that only a subset of fields is read as opposed to all fields?

If you read all fields, you can easily subset afterwards (again using 
$-notation).

hth,
Z

>> bib1 <- read.bib("C:/localtexmf/bibtex/bib/timeref.bib")
> ignoring entry 'Donoho-etal:1988' (line 40) because :
> A bibentry of bibtype ?InCollection? has to correctly specify the field(s): 
> booktitle
> ... snipping other similar warnings ...
>
>> length(bib1)
> [1] 628
>>
>> bib2 <- read.bib("W:/texmf/bibtex/bib/timeref.bib")
> ignoring entry 'Donoho-etal:1988' (line 57) because :
> A bibentry of bibtype ?InCollection? has to correctly specify the field(s): 
> booktitle
> ... snipping other similar warnings ...
>
>> length(bib2)
> [1] 611
>
> # The first bibentry:
>> bib1[[1]]
> Godfrey EH (1918). ?History and Development of Statistics in Canada.? In 
> Koren J (ed.), pp.
> 179-198. Macmillan, New York.
>> str(bib1[[1]])
> Class 'bibentry' hidden list of 1
> $ :List of 9
> ..$ author :Class 'person' hidden list of 1
> .. ..$ :List of 5
> .. .. ..$ given : chr [1:2] "Ernest" "H."
> .. .. ..$ family : chr "Godfrey"
> .. .. ..$ role : NULL
> .. .. ..$ email : NULL
> .. .. ..$ comment: NULL
> ..$ title : chr "History and Development of Statistics in {Canada}"
> ..$ booktitle: chr "History of Statistics, their Development and Progress in 
> Many Countries"
> ..$ publisher: chr "Macmillan"
> ..$ year : chr "1918"
> ..$ editor :Class 'person' hidden list of 1
> .. ..$ :List of 5
> .. .. ..$ given : chr "John"
> .. .. ..$ family : chr "Koren"
> .. .. ..$ role : NULL
> .. .. ..$ email : NULL
> .. .. ..$ comment: NULL
> ..$ pages : chr "179--198"
> ..$ address : chr "New York"
> ..$ crossref : chr "Koren:1918"
> ..- attr(*, "bibtype")= chr "InCollection"
> ..- attr(*, "key")= chr "Godfrey:1918"
>
> So, I try to get the "key" attribute for this entry, but it returns NULL, and 
> I don't understand why.
>> attr(bib1[[1]], "key")
> NULL
>> attr(bib1[1], "key")
> NULL
>
> -Michael
>
> -- 
> Michael Friendly     Email: friendly AT yorku DOT ca
> Professor, Psychology Dept.
> York University      Voice: 416 736-2100 x66249 Fax: 416 736-5814
> 4700 Keele Street    Web:   http://www.datavis.ca
> Toronto, ONT  M3J 1P3 CANADA
>
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