Classify occurrence records in levels of confidence in species identification

Classifies occurrence records in levels of confidence in species identification

classify_occ(
  occ,
  spec = NULL,
  na.rm.coords = TRUE,
  crit.levels = c("det_by_spec", "not_spec_name", "image", "sci_collection",
    "field_obs", "no_criteria_met"),
  ignore.det.names = NULL,
  spec.ambiguity = "not.spec",
  institution.code = "institutionCode",
  collection.code = "collectionCode",
  catalog.number = "catalogNumber",
  year = "year",
  date.identified = "dateIdentified",
  species = "species",
  identified.by = "identifiedBy",
  decimal.latitude = "decimalLatitude",
  decimal.longitude = "decimalLongitude",
  basis.of.record = "basisOfRecord",
  media.type = "mediaType",
  occurrence.id = "occurrenceID",
  institution.source,
  year.event,
  scientific.name,
  determined.by,
  latitude,
  longitude,
  basis.of.rec,
  occ.id
)

Arguments

occ	data frame with occurrence records information.
spec	data frame with specialists' names. See details.
na.rm.coords	logical. If `TRUE`, remove occurrences with `NA` in `decimal.latitude` or `decimal.longitude`
crit.levels	character. Vector with levels of confidence in decreasing order. The criteria allowed are `det_by_spec`, `not_spec_name`, `image`, `sci_collection`, `field_obs`, `no_criteria_met`. See details.
ignore.det.names	character vector indicating strings in `identified.by` that should be ignored as a taxonomist. See details.
spec.ambiguity	character. Indicates how to deal with ambiguity in specialists names. `not.spec` solve ambiguity by classifying the identification as done by a non-specialist;`is.spec` assumes the identification was done by a specialist; `manual.check` enables the user to manually check all ambiguous names. Default is `not.spec`.
institution.code	column name of `occ` with the name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.
collection.code	column name of `occ` with The name, acronym, code, or initials identifying the collection or data set from which the record was derived.
catalog.number	column name of `occ` with an identifier (preferably unique) for the record within the data set or collection.
year	Column name of `occ` the four-digit year in which the Event occurred, according to the Common Era Calendar.
date.identified	Column name of `occ` with the date on which the subject was determined as representing the Taxon.
species	column name of `occ` with the species names.
identified.by	column name of `occ` with the name of who determined the species.
decimal.latitude	column name of `occ` latitude in decimal degrees.
decimal.longitude	column name of `occ` longitude in decimal degrees.
basis.of.record	column name with the specific nature of the data record. See details.
media.type	column name of `occ` with the media type of recording. See details.
occurrence.id	column name of `occ` with link or code for the occurrence record. See in Darwin Core Format
institution.source	deprecated, use `institution.code` instead.
year.event	deprecated, use `year` instead.
scientific.name	deprecated, use `species` instead.
determined.by	deprecated, use `identified.by` instead
latitude	deprecated, use `decimal.latitude` instead
longitude	deprecated, use `decimal.longitude` instead
basis.of.rec	deprecated, use `basis.of.record` instead.
occ.id	deprecated, use `occurrence.id` instead

Value

The occ data frame plus the classification of each record in a new column, named naturaList_levels.

Details

spec data frame must have columns separating LastName, Name and Abbrev. See create_spec_df function for a easy way to produce this data frame.

When ignore.det.name = NULL (default), the function ignores strings with "RRC ID Flag", "NA", "", "-" and "_". When a character vector is provided, the function adds the default strings to the provided character vector and ignore all these strings as being a name of a taxonomist.

The function classifies the occurrence records in six levels of confidence in species identification. The six levels are:

det_by_spec - when the identification was made by a specialists which is present in the list of specialists provided in the spec argument;
not_spec_name - when the identification was made by a name who is not a specialist name provide in spec;
image - the occurrence have not name of a identifier, but present an image associated;
sci_collection - the occurrence have not name of a identifier, but preserved in a scientific collection;
field_obs - the occurrence have not name of a identifier, but it was identified in field observation;
no_criteria_met - no other criteria was met.

The (decreasing) order of the levels in the character vector determines the classification level order.

basis.of.record is a character vector with one of the following types of record: PRESERVED_SPECIMEN, PreservedSpecimen, HUMAN_OBSERVATION or HumanObservation, as in GBIF data 'basisOfRecord'.

media.type uses the same pattern as GBIF mediaType column, indicating the existence of an associated image with stillImage.

Author

Arthur V. Rodrigues

Examples