movepub 0.4.0

We released a new version of our R package movepub.

• Sanne Govaert

DTO-BioFlow software R
On this page

We just released a new version (0.4.0) of our R package movepub.

With movepub you prepare animal tracking data from Movebank for publication in a research repository. You can document data with metadata following the Data Package standard and transform these to Darwin Core and Ecological Metadata Language (EML) for publication to the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS).

What has changed?

We added two new functions:

  • write_eml() is now a separate function from write_dwc(). write_eml() now formats the derived_paragraph as DocBook (rather than HTML), a format supported by EML and the GBIF IPT.
  • html_to_docbook() allows to convert a string or character vector from HTML to DocBook. You can use this to convert descriptions in order to have valid EML.

We also updated write_dwc():

  • write_dwc() can now be used for an unpublished dataset (i.e. without metadata on DataCite, which was required for the previously build-in write_eml() functionality). Some record-level terms (e.g. dwc:datasetName) can be provided as arguments.
  • write_dwc() (and write_eml()) no longer writes to "." by default, since this is not allowed by CRAN policies. The user needs to explicitly define a directory.
  • write_dwc() now writes the output file as occurrence.csv (previously dwc_occurrence.csv) and adds a meta.xml file. The sex and life stage of the animal are - in addition to dwc:sex and dwc:lifeStage in occurrence.csv - expressed in an extended measurement or facts file (emof.csv), for better support with OBIS.
  • write_dwc() provides a message regarding the matching of scientific names with WoRMS Aphia IDs. These IDs are now clickable URLs, making it easier to verify the match.
  • write_dwc() is now more modular, facilitating extension for non-GPS tracking data.

And there are other changes:

  • movepub now relies on R >= 4.1.0 (because of move2 dependency) and uses base pipes (|> rather than %>%) (#98).
  • Many functions of frictionless are now reexported by movepub, so you no longer have to load that package to create Data Packages (#54).
  • get_mvb_term() is deprecated in favour of move2::movebank_get_vocabulary()

For a full overview of all the changes, see the CHANGELOG.

How to install movepub?

Want to use movepub in your work? The package is available on GitHub and can be installed with:

devtools::install_github("inbo/movepub")

For more information, see the package documentation. Found a bug? Please report an issue.