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Write EML metadata for a matched table

Source: R/eml.R
write_eml.Rd

Produces an Ecological Metadata Language document describing a table matchData() produced: what each column is, where and when it covers, which data sources went into it, and what to cite. EML is what repositories such as EDI and the LTER network expect alongside a deposited dataset.

Usage

write_eml(
  x,
  file,
  title,
  creator,
  abstract = NULL,
  contact = creator,
  keywords = NULL,
  entity_name = basename(file),
  validate = TRUE
)

Arguments

x

an sf object from matchData(), or any of the access functions

file

where to write the XML

title

the dataset's title

creator

a list in EML creator shape, or a character name. An ORCID is worth including; see the examples.

abstract

a paragraph on what the dataset is and why it exists

contact

the contact party; defaults to creator

keywords

optional keywords

entity_name

what the data file is called, for the dataTable

validate

validate against the EML schema before returning. Requires the emld package, and is worth leaving on: an invalid document is rejected at submission rather than at write time.

Value

the path, invisibly

What is filled in for you

Nearly all of it, because the package already knows:

  • Geographic coverage from the object's own bounding box.

  • Temporal coverage from its YEAR/MONTH/DAY columns.

  • An attribute for every column — definition, units, and measurement scale — with labels and units taken from whichever source catalog defines that name, and this package's own conventions used for the time, LON/LAT, <var>_source and <var>_depth columns.

  • Methods and citations from the <var>_source columns matchData() writes. This is the part worth having: a table with four sources chained onto it produces a methods section naming all four and a reference for each, rather than leaving you to reconstruct which fetch produced which column.

What it cannot know is who you are and what the dataset is for, so title, creator and abstract are yours to give.

Units, and why some are declared

EML validates units against a fixed vocabulary and rejects anything not on it. PSU and N/m2 are both absent from it — salinity and wind stress, two of this package's core variables — so they are written as custom units and declared in the document's own unitList. That is the mechanism EML provides for it, and the resulting document validates.

See also

matchData(), which writes the <var>_source columns this reads, and source_of()

Examples

if (FALSE) { # \dontrun{
matched <- matchData(observations, accessHYCOM(vars = "BOTS", ...))

write_eml(
  matched, "matched.xml",
  title = "Bottom salinity matched to trawl stations, Gulf of Maine",
  creator = list(individualName = list(givenName = "Camille",
                                       surName = "Ross"),
                 electronicMailAddress = "camille.ross@maine.edu",
                 userId = list(directory = "https://orcid.org",
                               userId = "0000-0002-1428-2294")),
  abstract = "Stations from the spring survey with HYCOM bottom salinity.")
} # }