Scott Chamberlain

Citations are a crucial piece of scholarly work. They hold metadata on
each scholarly work, including what people were involved, what year the
work was published, where it was published, and more. The links between
citations facilitate insight into many questions about scholarly work.

Citations come in [many different
formats](https://github.com/datacite/bolognese#features) including
BibTex, RIS, JATS, and many more. This is not to be confused with
[citation styles](https://citationstyles.org/) such as APA vs. MLA and
so on.

Those that deal with or do research on citations often get citations in
one format (e.g., BibTex), but they would like them in a different
format (e.g., RIS). One recent tool that does a very nice job of this is
[bolognese](https://github.com/datacite/bolognese) from [Martin
Fenner](https://github.com/mfenner) of
[Datacite](https://datacite.org/). `bolognese` is written in
[Ruby](https://www.ruby-lang.org/en/). I love the Ruby language, but it
does not play nicely with R; thus it wasn't an option to wrap or call
`bolognese` from R.

`handlr` is a new R package modeled after `bolognese`.

The original motivation for starting handlr comes from [this
thread](https://github.com/ropensci/rorcid/issues/51) in the
[rorcid](https://github.com/ropensci/rorcid) package, in which the
citations retrieved from source A had mangled characters with accents,
but source B gave un-mangled characters but in the wrong format. Thus
the need for a citation format converter.

handlr converts citations from one format to another. It currently
supports reading the following formats:

- [citeproc](https://en.wikipedia.org/wiki/CiteProc)
- [ris](https://en.wikipedia.org/wiki/RIS_(file_format))
- [bibtex](http://www.bibtex.org/)
- [codemeta](https://codemeta.github.io/)

And the following writers are supported:

- [citeproc](https://en.wikipedia.org/wiki/CiteProc)
- [ris](https://en.wikipedia.org/wiki/RIS_(file_format))
- [bibtex](http://www.bibtex.org/)
- [schema.org](https://schema.org/)
- [rdfxml](https://en.wikipedia.org/wiki/RDF/XML) (requires suggested
  package [jsonld](https://github.com/ropensci/jsonld/))
- [codemeta](https://codemeta.github.io/)

`handlr` has not yet focused on performance, but we will do so in future
versions.

Links:

- handlr source code: <https://github.com/ropensci/handlr>
- handlr on CRAN: <https://cran.rstudio.com/web/packages/handlr/>

## Installation

Install the lastest from CRAN

::: {.highlight}
``` {.chroma tabindex="0"}
install.packages("handlr")
```
:::

Some binaries are not up yet on CRAN - you can also install from
GitHub.There's no compiled code though, so source install should work.I
somehow forgot to export the `print.handl()` function in the CRAN
version, soif you try this with the CRAN version you won't get the
compact output seen below.

::: {.highlight}
``` {.chroma tabindex="0"}
remotes::install_github("ropensci/handlr")
```
:::

Load `handlr`

::: {.highlight}
``` {.chroma tabindex="0"}
library(handlr)
```
:::

## The R6 approach

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

grab an example file that comes with the package

::: {.highlight}
``` {.chroma tabindex="0"}
z <- system.file("extdata/citeproc.json", package = "handlr")
```
:::

initialize the object

::: {.highlight}
``` {.chroma tabindex="0"}
x <- HandlrClient$new(x = z)x#> <handlr> #>   doi: #>   ext: json#>   format (guessed): citeproc#>   path: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/handlr/extdata/citeproc.json#>   string (abbrev.): none
```
:::

read the file

::: {.highlight}
``` {.chroma tabindex="0"}
x$read(format = "citeproc")x#> <handlr> #>   doi: #>   ext: json#>   format (guessed): citeproc#>   path: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/handlr/extdata/citeproc.json#>   string (abbrev.): none
```
:::

inspect the parsed content

::: {.highlight}
``` {.chroma tabindex="0"}
x$parsed#> <handl> #>   from: citeproc#>   many: FALSE#>   count: 1#>   first 10 #>     id/doi: https://doi.org/10.5438/4k3m-nyvg
```
:::

write out to bibtex. by default does not write to a file; you canalso
specify a file path.

::: {.highlight}
``` {.chroma tabindex="0"}
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},#> }
```
:::

## Function approach

If you prefer not to use the above approach, you can use the
variousfunctions that start with he format (e.g., `bibtex`) followed
by`_reader` or `_writer`.

Here, we play with the bibtex format.

Get a sample file and use `bibtex_reader()` to read it in.

::: {.highlight}
``` {.chroma tabindex="0"}
z <- system.file('extdata/bibtex.bib', package = "handlr")bibtex_reader(x = z)#> <handl> #>   from: bibtex#>   many: FALSE#>   count: 1#>   first 10 #>     id/doi: https://doi.org/10.1142%2fs1363919602000495
```
:::

What this returns is a `handl` object, just a list with attributes.The
`handl` object is what we use as the internal representation that
weconvert citations to and from.

Each reader and writer supports handling many citations at once. For
allformats, this means many citations in the same file.

::: {.highlight}
``` {.chroma tabindex="0"}
z <- system.file('extdata/bib-many.bib', package = "handlr")bibtex_reader(x = z)#> <handl> #>   from: bibtex#>   many: TRUE#>   count: 2#>   first 10 #>     id/doi: https://doi.org/10.1093%2fbiosci%2fbiw022#>     id/doi: https://doi.org/10.1890%2f15-1397.1
```
:::

## To do

- There's still definitely some improvements that need to be made to
  various parts of citations in some of the formats. Do open an
  issue/let me know if you find anything off.
- Performance could be improved for sure
- Problems with very large files, e.g.,
  [ropensci/handlr#9](https://github.com/ropensci/handlr/issues/9)
- Documentation, there is very little thus far

## Get in touch

Get in touch if you have any `handlr` questions in the[issue
tracker](https://github.com/ropensci/handlr/issues) or the[rOpenSci
discussion forum](https://discuss.ropensci.org/).


Citations are a crucial piece of scholarly work. They hold metadata on each scholarly work, including what people were involved, what year the work was published, where it was published, and more. The links between citations facilitate insight into many questions about scholarly work. Citations come in many different formats including BibTex, RIS, JATS, and many more. This is not to be confused with citation styles such as APA vs. MLA and so on.

Rogue Scholar Beiträge

handlr: convert among citation formats