biblio

An R-package to manage bibliographic references. This package is focused on data import-export to a data frame format based on the software JabRef.

Installing biblio

You can install this package from GitHub.

library(remotes)
install_github("kamapu/biblio")

Reading Bibtex Files

A copy of the references cited in the book of Luebert & Pliscoff (2016) is also installed with this package.

library(biblio)
Bib <- read_bib(x = file.path(path.package("biblio"), "LuebertPliscoff.bib"))
Bib
#> Object of class 'lib_df'
#> 
#> Number of references: 1701
#> Number of variables: 23
#> Duplicated entries: 0
#> 
#> Pliscoff, P., Luebert, F. (2006). "Ecosistemas terrestres." In Rovira,
#> Jaime, Ugalde, Jaime, Stutzin, Miguel (eds.), _Biodiversidad de Chile:
#> Patrimonio y desafíos_, 74-8. Comisión Nacional de Medio Ambiente,
#> Santiago.
#> 
#> Luebert, F., Pliscoff, P. (200). _Clasificación de pisos de vegetación
#> y análisis de representatividad ecológica de áreas propuestas para la
#> protección en la ecorregión Valdiviana_. Documento N° 10, Serie de
#> Publicaciones WWF-Chile, Valdivia.
#> 
#> Pliscoff, P., Luebert, F. (2006). "Una nueva propuesta de clasificación
#> de la vegetación de Chile y su aplicación en la evaluación del estado
#> de conservación de los ecosistemas terrestres." _Ambiente y
#> Desarrollo_, *22*(1), 41-4.
#> 
#> Smith-Ramírez, C., Armesto, J. J, Rodríguez, J., Gutiérrez, G. A,
#> Christie, D., Núñez, M. (2005). "Aextoxicon punctatum, el tique u
#> olivillo." In _Historia, biodiversidad y ecología de los bosques
#> costeros de Chile_, 278-28. Editorial Universitaria, Santiago.
#> 
#> [TRUNCATED]

Scanning Cited References in R-Markdown Documents

An example of r-markdown document is also installed to test the function detect_keys(), which is able to recognize the bibtexkeys in use within an r-markdown document.

my_document <- readLines(file.path(path.package("biblio"), "document.Rmd"))
cited_refs <- detect_keys(my_document)
cited_refs
#>        bibtexkey line
#> 1 oberdorfer1960   10
#> 2     veblen1995   12
#> 3     veblen1996   12
#> 4 oberdorfer1960   15
#> 5 oberdorfer1960   19
#> 6     veblen1996   24
#> 7   pollmann2004   24
#> 8    ramirez2005   29

Alternatively to the last option, you can use the function read_rmd() from the package yamlme. Note that in this case the position of the citation may change because detect_keys() will start counting lines after the yaml-header.

library(yamlme)
my_document <- read_rmd(file.path(path.package("biblio"), "document.Rmd"))
cited_refs <- detect_keys(my_document)
#> Lines are counted only at the body of the document.
cited_refs
#>        bibtexkey line
#> 1 oberdorfer1960    4
#> 2     veblen1995    6
#> 3     veblen1996    6
#> 4 oberdorfer1960    9
#> 5 oberdorfer1960   13
#> 6     veblen1996   18
#> 7   pollmann2004   18
#> 8    ramirez2005   23

The output shows the respective bibtexkey by its occurrence in the document (line number). With this output it is also possible to do some statistics.

stats_refs <- aggregate(line ~ bibtexkey, data = cited_refs, FUN = length)

# Number of citations in text
sum(stats_refs$line)
#> [1] 8

# Number of cited articles
nrow(stats_refs)
#> [1] 5

# Respective frequency to know rare citations in text
stats_refs[order(stats_refs$line, decreasing = TRUE), ]
#>        bibtexkey line
#> 1 oberdorfer1960    3
#> 5     veblen1996    2
#> 2   pollmann2004    1
#> 3    ramirez2005    1
#> 4     veblen1995    1

Automatic Reference Lists

The package yamlme enables the use of functions to write R-markdown documents and to render them. In this context, the function reflist() will produce automatically a reference list.

Bib2 <- subset(x = Bib, subset = as.integer(year) > 2005)
reflist(obj = Bib2, filename = "my_reflist")

Note that assigning the output of reflist() to a new object and using the package yamlme, you may be able to modify the layout by using the function update(). Remember to set

library(yamlme)

# Subset and assignment
Bib2 <- subset(x = Bib, subset = as.integer(year) > 2005)
my_reflist <- reflist(x = Bib2, filename = "my_reflist", browse_file = FALSE)

# Updating and rendering
my_reflist <- update(
  object = my_reflist,
  title = "Reference List (PDF version)",
  author = "myself",
  output = "pdf_document",
  body = txt_body(
    "\\setlength{\\parindent}{-5mm}",
    "\\setlength{\\leftskip}{5mm}",
    "\\setlength{\\parskip}{8pt}"
  )
)
render_rmd(my_reflist, output_file = "my_reflist")

Note that rendering the updated document will also require the written bibtex file, thus sharing an input bibtexfile or an lib_df object within an R-image may be the most secure way to enable repeatability.