A Simple Author Handler for Scientific Writing

Handles and formats author information in scientific writing in 'R Markdown' and 'Quarto'. 'plume' provides easy-to-use and flexible tools for inserting author data in 'YAML' as well as generating author and contribution lists (among others) as strings from tabular data.

plume

Overview

plume provides tools for handling and generating author-related information for scientific writing in R Markdown and Quarto. The package implements two R6 classes:

• PlumeQuarto: class that allows you to add or update author metadata in YAML files or the YAML header of Quarto documents. The generated YAML complies with Quarto’s author and affiliations schemas. This is the class to use when working with journal templates.

• Plume: class that generates author lists and other author-related information as character vectors. This is a simple and convenient solution when you don’t need preformatted documents.

Installation

Install plume from CRAN with:

install.packages("plume")

Alternatively, you can install the development version of plume from GitHub with:

# install.packages("pak")
pak::pak("arnaudgallou/plume")

Usage

The minimal required data to work with plume classes is a dataset containing given and family names but you would normally want to provide more information such as email addresses, ORCIDs, affiliations, etc.

library(plume)

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$new(encyclopedists)
#> # A tibble: 4 × 11
#>      id given_name     family_name literal_name initials orcid email phone note 
#>   <int> <chr>          <chr>       <chr>        <chr>    <chr> <chr> <chr> <chr>
#> 1     1 Denis          Diderot     Denis Dider… D.D.     0000… dide… +1234 born…
#> 2     2 Jean-Jacques   Rousseau    Jean-Jacque… J.-J.R.  0000… rous… <NA>  <NA> 
#> 3     3 François-Marie Arouet      François-Ma… F.-M.A.  <NA>  arou… <NA>  also…
#> 4     4 Jean           Le Rond d'… Jean Le Ron… J.L.R.d… 0000… alem… <NA>  born…
#> # ℹ 2 more variables: affiliation <list>, role <list>

PlumeQuarto lets you insert author data into YAML files or the YAML header of any .qmd document using the to_yaml() method.

Consider the following example:

---
title: Encyclopédie
---

Qui scribit bis legit

aut <- PlumeQuarto$new(
  encyclopedists,
  file = "example.qmd"
)
aut$set_corresponding_authors(1, 4)
aut$to_yaml()

---
title: Encyclopédie
author:
  - id: aut1
    name:
      given: Denis
      family: Diderot
    email: [email protected]
    phone: '+1234'
    orcid: 0000-0000-0000-0001
    note: born in 1713 in Langres
    attributes:
      corresponding: true
    roles:
      - Supervision
      - Writing - original draft
    affiliations:
      - ref: aff1
  - id: aut2
    name:
      given: Jean-Jacques
      family: Rousseau
    email: [email protected]
    orcid: 0000-0000-0000-0002
    attributes:
      corresponding: false
    roles:
      - Writing - original draft
    affiliations:
      - ref: aff2
  - id: aut3
    name:
      given: François-Marie
      family: Arouet
    email: [email protected]
    note: also known as Voltaire
    attributes:
      corresponding: false
    roles:
      - Writing - original draft
    affiliations:
      - ref: aff2
  - id: aut4
    name:
      given: Jean
      family: Le Rond d'Alembert
    email: [email protected]
    orcid: 0000-0000-0000-0003
    note: born in 1717 in Paris
    attributes:
      corresponding: true
    roles:
      - Supervision
      - Writing - original draft
    affiliations:
      - ref: aff1
      - ref: aff3
affiliations:
  - id: aff1
    name: Université de Paris
  - id: aff2
    name: Lycée Louis-le-Grand
  - id: aff3
    name: Collège des Quatre-Nations
---

Qui scribit bis legit

Alternatively, you can generate author information as character vectors using Plume:

aut <- Plume$new(encyclopedists)
aut$set_corresponding_authors(diderot, .by = "family_name")

aut$get_author_list(suffix = "^a,^cn")
#> Denis Diderot^1,^\*†
#> Jean-Jacques Rousseau^2^
#> François-Marie Arouet^2^‡
#> Jean Le Rond d'Alembert^1,3^§

aut$get_contact_details()
#> [email protected] (Denis Diderot)

aut$get_affiliations()
#> ^1^Université de Paris
#> ^2^Lycée Louis-le-Grand
#> ^3^Collège des Quatre-Nations

aut$get_notes()
#> ^†^born in 1713 in Langres
#> ^‡^also known as Voltaire
#> ^§^born in 1717 in Paris

aut$get_contributions()
#> Supervision: D.D. and J.L.R.d'A.
#> Writing - original draft: D.D., J.-J.R., F.-M.A. and J.L.R.d'A.

aut2 <- Plume$new(
  encyclopedists,
  roles = c(
    supervision = "supervised the project",
    writing = "contributed to the Encyclopédie"
  ),
  symbols = plm_symbols(affiliation = letters)
)

aut2$get_author_list("^a^")
#> Denis Diderot^a^
#> Jean-Jacques Rousseau^b^
#> François-Marie Arouet^b^
#> Jean Le Rond d'Alembert^a,c^

aut2$get_contributions(roles_first = FALSE, divider = " ")
#> D.D. and J.L.R.d'A. supervised the project
#> D.D., J.-J.R., F.-M.A. and J.L.R.d'A. contributed to the Encyclopédie

Acknowledgements

Thanks to:

• Richard J. Telford for his advice that helped me conceive this package.

• Maëlle Salmon and Gábor Csárdi for their help when I was stuck with unit tests, roxygen2 or pkgdown.