paperbark

Overview

paperbark is a package for import and type conversion of metadata statements. Its purpose is to enable users to store metadata in markdown files, and convert them to EML. It is named for the peeling growth form displayed by a number of Australian plant species. The logo was drawn by Martin Westgate, and shows the flower of the swamp paperbark Melaleuca ericifolia.

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Installation

This package is under active development, and is not yet available on CRAN. You can install the latest development version from GitHub with:

install.packages("remotes")
remotes::install_github("AtlasOfLivingAustralia/paperbark")

Load the package:

library(paperbark)

Basic usage

The primary use case for paperbark is to manipulate the format of metadata statements for sharing biodiversity data. The first step is to create a markdown file, and add any headings that you like that conform to the EML standard. The header ‘level’ (i.e. number of #) is used to designate the degree of nesting. If you don’t want to start from scratch, you can use the example dataset metadata_example:

library(dplyr)
metadata_example |>
  slice_head(n = 5)
#> # A tibble: 5 × 4
#>   level label    text                                               attributes  
#>   <dbl> <chr>    <chr>                                              <list>      
#> 1     1 eml:eml  <NA>                                               <named list>
#> 2     2 Dataset  <NA>                                               <lgl [1]>   
#> 3     3 Title    A Sentence Giving Your Dataset Title In Title Case <lgl [1]>   
#> 4     3 Abstract A paragraph outlining the content of the dataset   <lgl [1]>   
#> 5     3 Creator  <NA>                                               <lgl [1]>

It is straightforward to export this to your working directory using write_md():

write_md(metadata_example, "metadata.md")

Once you are done, import it to R using read_md(). It will be stored as a tibble:

x <- read_md("metadata.md")
x 

#> # A tibble: 29 × 4
#>    level label                  text                                attributes  
#>    <dbl> <chr>                  <chr>                               <list>      
#>  1     1 eml:eml                <NA>                                <named list>
#>  2     2 dataset                <NA>                                <lgl [1]>   
#>  3     3 title                  <NA>                                <lgl [1]>   
#>  4     4 <NA>                   An awesome dataset                  <NULL>      
#>  5     2 description            <NA>                                <lgl [1]>   
#>  6     3 <NA>                   This data is the best. You should … <NULL>      
#>  7     3 publicShortDescription <NA>                                <lgl [1]>   
#>  8     3 publicDescription      <NA>                                <lgl [1]>   
#>  9     3 technicalDescription   <NA>                                <lgl [1]>   
#> 10     3 dataQualityDescription <NA>                                <lgl [1]>   
#> # ℹ 19 more rows

You can then export it as an xml file without any intermediate steps:

write_eml(x, "metadata.xml")

For a more detailed description of paperbark’s capabilities and methods, see the ‘Quick start guide’ vignette.

Citing paperbark

To generate a citation for the package version you are using, you can run:

citation(package = "paperbark")

The current recommended citation is:

Westgate MJ, Balasubramaniam S & Kellie D (2024) paperbark: Convert markdown files to EML. R Package version 0.1.0.