The goal of the plume package is to make the handling and formatting of author data for scientific writing in R Markdown and Quarto easy and painless.
We’ll use the data sets encyclopedists and
encyclopedists_fr to explore the different functionalities
of the package. These data sets contain information on four famous
authors of the “Encyclopédie”, published in France in the 18th century.
encyclopedists_fr is the French translation of
encyclopedists and will be used to illustrate how to handle
custom variable names. Both data sets are documented in
?encyclopedists.
encyclopedists
#> # A tibble: 4 × 10
#> given_name family_name email phone orcid supervision writing note
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr>
#> 1 Denis Diderot dider… +1234 0000… 1 1 born…
#> 2 Jean-Jacques Rousseau rouss… <NA> 0000… NA 1 <NA>
#> 3 François-Marie Arouet aroue… <NA> <NA> NA 1 also…
#> 4 Jean Le Rond d'Alembert alemb… <NA> 0000… 1 1 born…
#> # ℹ 2 more variables: affiliation_1 <chr>, affiliation_2 <chr>plume objectplume provides two R6 classes, namely Plume and
PlumeQuarto. To create a plume object, simply
write the name of the class you want to use followed by the
new() method. plume classes take a data frame or tibble as
input data. The input data must have at least two columns, one for given
names and another for family names.
Plume$new(encyclopedists)
#> # A tibble: 4 × 11
#> id given_name family_name literal_name initials email phone orcid note
#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1 Denis Diderot Denis Dider… DD dide… +1234 0000… born…
#> 2 2 Jean-Jacques Rousseau Jean-Jacque… J-JR rous… <NA> 0000… <NA>
#> 3 3 François-Marie Arouet François-Ma… F-MA arou… <NA> <NA> also…
#> 4 4 Jean Le Rond d'… Jean Le Ron… JLRd'A alem… <NA> 0000… born…
#> # ℹ 2 more variables: affiliation <list>, role <list>The default variables handled by plume classes are organised into six categories:
Primaries: variables required to create a
plume object.
| Name | Plume | PlumeQuarto |
|---|---|---|
| given_name | ||
| family_name |
Secondaries: optional variables that can be provided in the input data.
| Name | Plume | PlumeQuarto |
|---|---|---|
| phone | ||
| fax | ||
| url | ||
| number | ||
| dropping_particle | ||
| acknowledgements |
Nestables: optional variables that can be provided
in the input data to pass multiple independent values to authors.
Nestable variables must start with the same prefix. E.g.
affiliation_1, affiliation_2, …,
affiliation_n to pass several affiliations to authors.
| Name | Plume | PlumeQuarto |
|---|---|---|
| affiliation | ||
| role | ||
| note | ||
| degree |
Constants: optional names that can be provided in the input data. These names are standardised and must be provided as is.
| Name | Plume | PlumeQuarto |
|---|---|---|
| orcid | ||
| conceptualization | ||
| data_curation | ||
| analysis | ||
| funding | ||
| investigation | ||
| methodology | ||
| administration | ||
| resources | ||
| software | ||
| supervision | ||
| validation | ||
| visualization | ||
| writing | ||
| editing |
Internals: variables created internally. These variables don’t need to be provided in the input data and are ignored if supplied. You shouldn’t worry much about these variables unless you want to customise names or extend plume classes with new default names.
| Name | Plume | PlumeQuarto |
|---|---|---|
| id | ||
| initials | ||
| literal_name | ||
| corresponding | ||
| contributor_rank | ||
| deceased | ||
| equal_contributor |
Meta: PlumeQuarto-specific variables
used to pass extra information that doesn’t fit in other categories.
Meta columns must start with the prefix meta- and are
followed by a custom name (e.g. meta-custom_name). You
should only use these variables to pass data that are template specific.
See Quarto’s arbitrary-metadata
section for details.
plume lets you use custom variable names. Simply provide the
names parameter a named vector when instantiating a plume
class, where keys are default names and values their respective
replacements.
Plume$new(
encyclopedists_fr,
names = c(
given_name = "prénom",
family_name = "nom",
literal_name = "nom_complet",
email = "courriel",
initials = "initiales"
)
)
#> # A tibble: 4 × 10
#> id prénom nom nom_complet initiales courriel orcid role note
#> <int> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1 Denis Diderot Denis Dide… DD diderot… 0000… Supe… né e…
#> 2 2 Jean-Jacques Rousseau Jean-Jacqu… J-JR roussea… 0000… <NA> <NA>
#> 3 3 François-Marie Arouet François-M… F-MA arouet@… <NA> <NA> dit …
#> 4 4 Jean Le Rond… Jean Le Ro… JLRd'A alember… 0000… Supe… né e…
#> # ℹ 1 more variable: affiliation <list>You can add roles by creating specific role columns in the input data
and indicate contributors using 1:
#> # A tibble: 4 × 4
#> given_name family_name supervision writing
#> <chr> <chr> <dbl> <dbl>
#> 1 Denis Diderot 1 1
#> 2 Jean-Jacques Rousseau NA 1
#> 3 François-Marie Arouet NA 1
#> 4 Jean Le Rond d'Alembert 1 1plume uses the Contributor Roles
Taxonomy (CRediT) by default (assuming the input data contains the
appropriate columns). You can specify your own
roles via the roles parameter when creating a
plume object. The roles parameter takes a
vector of key-value pairs where keys identify role columns and values
define the actual roles to use.
PlumeQuarto allows you to inject author metadata
directly into YAML files or the YAML header of .qmd
files.
Consider the following Quarto document:
---
title: Encyclopédie
---
Qui scribit bis legitYou can push information from the input data into the YAML or Quarto
file using the to_yaml() method:
---
title: Encyclopédie
author:
- id: aut1
name:
given: Denis
family: Diderot
email: diderot@encyclopediste.fr
phone: '+1234'
orcid: 0000-0000-0000-0001
note: born in 1713 in Langres
roles:
- Supervision
- Writing - original draft
affiliations:
- ref: aff1
- id: aut2
name:
given: Jean
family: Le Rond d'Alembert
email: alembert@encyclopediste.fr
orcid: 0000-0000-0000-0003
note: born in 1717 in Paris
roles:
- Supervision
- Writing - original draft
affiliations:
- ref: aff1
- ref: aff2
affiliations:
- id: aff1
name: Université de Paris
- id: aff2
name: Collège des Quatre-Nations
---
Qui scribit bis legitAuthors are listed in the order they’re defined in the input data.
If the YAML or Quarto file already has an author and
affiliations keys, to_yaml() replaces old
values with new ones.
---
title: Encyclopédie
author:
- name:
given: Jean-Jacques
family: Rousseau
email: rousseau@encyclopediste.fr
orcid: 0000-0000-0000-0002
roles:
- Writing - original draft
affiliations:
- ref: aff1
affiliations:
- id: aff1
name: Lycée Louis-le-Grand
---
Qui scribit bis legitDefault symbols are:
#> List of 3
#> $ affiliation : NULL
#> $ corresponding: chr "\\*"
#> $ note : chr [1:6] "†" "‡" "§" "¶" "#" "\\*\\*"You can change symbols when creating a plume object
using the parameter symbols.
Use NULL to display numbers:
aut <- Plume$new(
encyclopedists,
symbols = list(affiliation = letters, note = NULL)
)
aut$get_author_list("^a,n^")
#> Denis Diderot^a,1^
#> Jean-Jacques Rousseau^b^
#> François-Marie Arouet^b,2^
#> Jean Le Rond d'Alembert^a,c,3^Use NULL as much as possible for symbols using numerous
unique items (typically affiliations). If you have to use letters for a
given category that has more unique items than letters, you can control
the sequencing behaviour using the sequential() modifier,
as shown below:
By default, plume repeats elements when all elements in a vector are
consumed. Using sequential() allows you to display a
logical sequence of characters
(e.g. a, b, c, ..., z, aa, ab, ac, ..., az, ba, bb, bc, ...).
To output author data as markdown content, use the chunk option
results: asis in combination with cat():
Inline chunks output values “as is” by default and can be used as follows:
`r aut$get_author_list()`