handlr

Scott Chamberlain

2020-10-14

handlr: convert among citation formats

heavily influenced by, and code ported from https://github.com/datacite/bolognese

supported readers:

• citeproc
• ris
• bibtex (requires suggested package bibtex)
• codemeta
• cff

supported writers:

• citeproc
• ris
• bibtex
• schema.org
• rdfxml (requires suggested package jsonld)
• codemeta
• cff

not supported yet, but plan to:

• crosscite

Installation

stable version

install.packages("handlr")
# OR
install.packages("handlr", repos = "https://dev.ropensci.org")

dev version

remotes::install_github("ropensci/handlr")

library("handlr")

All in one

There’s a single R6 interface to all readers and writers

z <- system.file("extdata/citeproc.json", package = "handlr")
x <- HandlrClient$new(x = z)
x
#> <handlr> 
#>   doi: 
#>   ext: json
#>   format (guessed): citeproc
#>   path: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/handlr/extdata/citeproc.json
#>   string (abbrev.): none

read the file

x$read(format = "citeproc")

the parsed content

x$parsed
#> <handl> 
#>   from: citeproc
#>   many: FALSE
#>   count: 1
#>   first 10 
#>     id/doi: https://doi.org/10.5438/4k3m-nyvg

write out bibtex

cat(x$write("bibtex"), sep = "\n")
#> @article{https://doi.org/10.5438/4k3m-nyvg,
#>   doi = {10.5438/4k3m-nyvg},
#>   author = {Martin Fenner},
#>   title = {Eating your own Dog Food},
#>   journal = {DataCite Blog},
#>   pages = {},
#>   publisher = {DataCite},
#>   year = {2016},
#> }

Choose your own adventure

Instead of using the HandlrClient, you can use the regular functions for each reader or writer. They are:

• citeproc_reader() / citeproc_writer()
• ris_reader() / ris_writer()
• bibtex_reader() / bibtex_writer()
• codemeta_reader() / codemeta_writer()
• schema_org_writer()
• rdf_xml_writer()

Convert data to data.frame

z <- system.file('extdata/bib-many.bib', package = "handlr")
res2 <- bibtex_reader(x = z)
handl_to_df(res2)
#>             key                                        id    type bibtex_type
#> 1    Amano_2016 https://doi.org/10.1093%2fbiosci%2fbiw022 article     article
#> 2 Bachelot_2016       https://doi.org/10.1890%2f15-1397.1 article     article
#>     citeproc_type ris_type resource_type_general additional_type
#> 1 article-journal     JOUR                  <NA>  JournalArticle
#> 2 article-journal     JOUR                  <NA>  JournalArticle
#>                     doi                                   b_url
#> 1 10.1093/biosci/biw022 http://dx.doi.org/10.1093/biosci/biw022
#> 2     10.1890/15-1397.1     http://dx.doi.org/10.1890/15-1397.1
#>                                                                                                        title
#> 1                            Spatial Gaps in Global Biodiversity Information and the Role of Citizen Science
#> 2 Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests
#>                                                                                           author
#> 1                                                            Amano T., Lamming J., Sutherland W.
#> 2 Bachelot B., Uriarte M., Zimmerman J., Thompson J., Leff J., Asiaii A., Koshner J., McGuire K.
#>                         publisher                         is_part_of
#> 1 Oxford University Press ({OUP})            Periodical;{BioScience}
#> 2                 Wiley-Blackwell Periodical;Ecological Applications
#>   date_published volume first_page last_page    state
#> 1           <NA>     66        393       400 findable
#> 2           <NA>   <NA>       <NA>      <NA> findable