prepDup: Prepare For Duplicate Specimen Search

In LimaRAF/plantR: Managing Species Records from Biological Collections

Prepare For Duplicate Specimen Search

Description

This function creates the duplicate search strings by concatenating the information on the taxonomy, collection and locality of the records.

Usage

prepDup(
  x,
  col.names = c(family = "family.new", species = "scientificName.new", col.name =
    "recordedBy.new", col.last.name = "last.name", col.number = "recordNumber.new",
    col.year = "year.new", col.loc = "municipality.new", loc.str = "loc.correct"),
  comb.fields = list(c("family", "col.last.name", "col.number", "col.loc"), c("family",
    "col.year", "col.number", "col.loc"), c("species", "col.last.name", "col.number",
    "col.year"), c("col.year", "col.last.name", "col.number", "col.loc")),
  rec.ID = "numTombo",
  noYear = "s.d.",
  noName = "s.n.",
  noNumb = "s.n.",
  ignore.miss = TRUE
)

Arguments

x	a data frame with the species records.
col.names	vector. A named vector containing the names of columns in the input data frame for each of the information that should be used to create the duplicate search string(s). Default to the plantR output column names.
comb.fields	list. A list containing one or more vectors with the information that should be used to create the duplicate search strings. Default to four vectors of information to be combined.
rec.ID	character. The name of the columns containing the unique record identifier (see function getTombo()). Default to 'numTombo'.
noYear	character. Standard for missing data in Year. Default to "n.d.".
noName	character. Standard for missing data in collector name. Default to "s.n.".
noNumb	character. Standard for missing data in collector number. Default to "s.n.".
ignore.miss	logical. Should the duplicate search strings with missing/unknown information (e.g. 'n.d.', 's.n.', NA) be excluded from the duplicate search. Default to TRUE.

Details

Three groups of fields are available to produce the duplicate search string, and they are related to taxonomy, collection and locality of the specimen. These fields should be provided to the argument col.names and they are:

• 'family': the botanical family (default: 'family.new')

• 'species': the scientific name (default: 'scientificName.new')

• 'col.name': the collector name (default: 'recordedBy.new')

• 'col.last.name': the collector last name (default: 'last.name')

• 'col.number': the collector serial number (default: 'recordNumber.new')

• 'col.year': the collection year (default: 'year.new')

• 'col.loc': the collection locality (default: 'municipality.new')

The corresponding columns that should be used to retrieve these fields in the input data frame must be provided as a named vector in the argument col.names, in which the fields listed above are the names and each element is the corresponding column name in the input data frame.

If an element named 'loc.str' containing the column name of the plantR locality string (i.e. 'loc.correct') is also provided, it can be used to complement any missing locality information in the locality of the collection (i.e 'col.loc') that may have been retrieved in the data processing within the plantR workflow.

The duplicate search strings are created by combining the fields listed above. Each combination of those fields (e.g. 'col.name' and 'col.number') should be provided to the argument comb.fields as a vector within a list. The number of strings to be generated will correspond to the number of vectors in this list. The order of the fields within vectors does not change the duplicate search process.

The argument rec.ID should indicate the column name in the input data containing the unique record identifier, which in the plantR workflow is obtained using the function getTombo(). If only GBIF data is used, this column could be the field 'gbifID'. This identifier is used to indicate the groups of duplicated records, which is one of the outputs of function getDup() and is used to homogenize information within the groups of duplicates (function mergeDup()).

Please note that the retrieval of duplicates greatly depends on the completeness of the input information and in the amount of differences of notation standards among collections. In addition, the smaller the vectors of fields to be combined to create the duplicate strings, the higher the number of (true and false) duplicates will be retrieved.

Author(s)

Renato A. F. de Lima

See Also

getTombo, getDup and mergeDup.

LimaRAF/plantR documentation built on Jan. 1, 2023, 10:18 a.m.