Create metadata template — create

This function creates a metadata template to be used in format_columns() for formatting and standardizing column names and classes in occurrence datasets. All column names specified as arguments must be present in the occ dataset.

If you obtained data from GBIF, SpeciesLink, BIEN or iDigBio using the functions provided in the RuHere package, you do not need to use this function, as the package already includes metadata templates for these datasets.

Usage

create_metadata(
  occ,
  scientificName,
  decimalLongitude,
  decimalLatitude,
  collectionCode = NA,
  catalogNumber = NA,
  coordinateUncertaintyInMeters = NA,
  elevation = NA,
  country = NA,
  stateProvince = NA,
  municipality = NA,
  locality = NA,
  year = NA,
  eventDate = NA,
  recordedBy = NA,
  identifiedBy = NA,
  basisOfRecord = NA,
  occurrenceRemarks = NA,
  habitat = NA,
  datasetName = NA,
  datasetKey = NA,
  key = NA
)

Arguments

occ: (data.frame or data.table) a dataset with occurrence records to be standardized.
scientificName: (character) column name in occ with the scientific name of the species.
decimalLongitude: (character) column name in occ with the longitude.
decimalLatitude: (character) column name in occ with the latitude.
collectionCode: (character) an optional column name in occ with the collection code.
catalogNumber: (character) an optional column name in occ with the catalog number.
coordinateUncertaintyInMeters: (character) an optional column name with the coordinate uncertainty in meters.
elevation: (character) an optional column name with the elevation information.
country: (character) an optional column name with the country of the record.
stateProvince: (character) an optional column name with the state or province of the record.
municipality: (character) an optional column name with the municipality of the record.
locality: (character) an optional column name with the locality description.
year: (character) an optional column name with the year when the occurrence was recorded.
eventDate: (character) an optional column name with the event date.
recordedBy: (character) an optional column name with the name of the collector or recorder.
identifiedBy: (character) an optional column name with the name of the identifier.
basisOfRecord: (character) an optional column name with the basis of record.
occurrenceRemarks: (character) an optional column name with remarks about the occurrence.
habitat: (character) an optional column name with the habitat description.
datasetName: (character) an optional column name with the dataset name.
datasetKey: (character) an optional column name with the dataset key.
key: (character) an optional column name with the unique occurrence identifier.

Value

A data.frame containing a metadata template that can be directly used in the format_columns() function.

Examples

# Load data example
# Occurrences of Puma concolor from the atlanticr R package
data("puma_atlanticr", package = "RuHere")
# Create metadata to standardize the occurrences
puma_metadata <- create_metadata(occ = puma_atlanticr,
                                 scientificName = "actual_species_name",
                                 decimalLongitude = "longitude",
                                 decimalLatitude = "latitude",
                                 elevation = "altitude",
                                 country = "country",
                                 stateProvince = "state",
                                 municipality = "municipality",
                                 locality = "study_location",
                                 year = "year_finish",
                                 habitat = "vegetation_type",
                                 datasetName = "reference")
# Now, we can use this metadata to standardize the columns
puma_occ <- format_columns(occ = puma_atlanticr, metadata = puma_metadata,
                           binomial_from = "actual_species_name",
                           data_source = "atlanticr")
#> Warning: NAs introduced by coercion