elm

Overview

elm is a package for import and type conversion of metadata statements. It’s function is to enable users to store metadata in markdown files, and convert them to EML.

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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/elm")

Load the package:

library(elm)

Basic usage

The basic use case for elm is to import metadata to a tibble, for example from a markdown file:

x <- system.file("example_data", 
                 "README_md_example.md", 
                 package = "elm") |>
  read_elm()

x 
#> # A tibble: 28 × 4
#>    level label                  text                                  attributes
#>    <dbl> <chr>                  <chr>                                 <list>    
#>  1     2 dataset                <NA>                                  <lgl [1]> 
#>  2     3 title                  <NA>                                  <lgl [1]> 
#>  3     4 <NA>                   An awesome dataset                    <NULL>    
#>  4     2 description            <NA>                                  <lgl [1]> 
#>  5     3 <NA>                   This data is the best. You should us… <NULL>    
#>  6     3 publicShortDescription <NA>                                  <lgl [1]> 
#>  7     3 publicDescription      <NA>                                  <lgl [1]> 
#>  8     3 technicalDescription   <NA>                                  <lgl [1]> 
#>  9     3 dataQualityDescription <NA>                                  <lgl [1]> 
#> 10     3 methodsDescription     <NA>                                  <lgl [1]> 
#> # ℹ 18 more rows

or alternatively from xml:

read_elm("https://collections.ala.org.au/ws/eml/dr368")
#> # A tibble: 85 × 4
#>    level label                text                                  attributes  
#>    <int> <chr>                <chr>                                 <list>      
#>  1     1 Eml                  <NA>                                  <named list>
#>  2     2 Dataset              <NA>                                  <named list>
#>  3     3 Alternate Identifier <NA>                                  <lgl [1]>   
#>  4     4 <NA>                 0101d74b-afc2-3b0f-817c-dc350d2a6fe4  <lgl [1]>   
#>  5     4 <NA>                 10.15468/14jd9g                       <lgl [1]>   
#>  6     4 <NA>                 0645ccdb-e001-4ab0-9729-51f1755e007e  <lgl [1]>   
#>  7     4 <NA>                 https://collections.ala.org.au/publi… <lgl [1]>   
#>  8     3 Title                <NA>                                  <named list>
#>  9     4 <NA>                 NSW BioNet Atlas                      <lgl [1]>   
#> 10     3 Creator              <NA>                                  <named list>
#> # ℹ 75 more rows

Here it can be examined and modified as required, then exported to either format:

write_elm(x, "metadata.xml")

For a more detailed description of elm’s capabilities and methods, see the ‘elm architecture’ vignette.

Citing elm

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

citation(package = "elm")

The current recommended citation is:

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